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US20120149714A1 - Effects of Inhibitors of FGFR3 on Gene Transcription - Google Patents

Effects of Inhibitors of FGFR3 on Gene Transcription Download PDF

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Publication number
US20120149714A1
US20120149714A1 US13/400,833 US201213400833A US2012149714A1 US 20120149714 A1 US20120149714 A1 US 20120149714A1 US 201213400833 A US201213400833 A US 201213400833A US 2012149714 A1 US2012149714 A1 US 2012149714A1
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patient
biomarker
protein
treatment
alteration
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US13/400,833
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Carla Heise
Esther Masih-Khan
Edward Moler
Michael Rowe
Keith Stewart
Suzanne Trudel
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/136—Screening for pharmacological compounds
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • Proliferative cell disorders such as cancers usually develop through the accumulation of a series of mutations in the patient's DNA within a subpopulation of cells. These mutations may confer a survival advantage on the cells that causes them to grow and spread in an uncontrolled manner that is deleterious to the surrounding tissues.
  • the particular set of mutations may be unique to an individual patient's tumor. Cancers of the same tissue or organ in different individuals may have originated from different sets of mutations, though certain mutations may be prevalent among particular cancer types. The characteristic set of mutations will determine how the cancer cells behave, and in particular, their likelihood of response to a given therapeutic regimen.
  • One main purpose is to determine which variations in individuals or subpopulations, associated with their genetics or the genetic characteristics of their disease, factor into drug efficacy and to create suitable tests, including diagnostic tests. Drugs that are tailored for patients with a particular genetic sequence, or for diseases characterized by particular genetic alterations, may thus be produced.
  • the tests may also be used to guide treatment decisions, such as which drug or drug combination is mostly likely to be beneficial to the patient, and what dosing and schedule is most appropriate. Diagnostic tests and genetic profiling will help avoid the expense and the potentially detrimental trial-and-error approach to the suitability of a particular treatment regimen or a particular dosage level.
  • This approach may be extended to mutations that are specific to cancer cells, and not otherwise found in the patient's genome. For instance, it has been demonstrated clinically in patients with gastrointestinal stromal tumors (GIST) treated with the drug Gleevec (imatinib mesylate; Novartis) that particular activating mutations in the genes KIT and PDGFA are linked to higher response rates to the drug, see J Clin Oncol. 2003 Dec. 1; 21(23):4342-9.
  • GIST gastrointestinal stromal tumors
  • One embodiment of the invention relates to a method of identifying a patient for treatment.
  • the method may optionally include an administration of an FGFR3 inhibitor to the patient prior to measurement of gene expression on a sample obtained from the patient.
  • the gene expression analysis is intended to detect the presence and/or alteration in level of expression of biomarkers disclosed herein. Notable detection or alteration in the levels compared to baseline levels is indicative of the candidacy of the patient for treatment.
  • Another embodiment of the invention comprises a method of monitoring response of a patient to treatment.
  • the method may include the step of administration of an FGFR3 inhibitor to the patient prior to measurement of gene expression on a sample obtained from the patient.
  • monitoring may be conducted on a sample obtained from a patient who has previously been treated so that an administration step by one practicing the method of monitoring response is not required. Detection of an alteration in the level of expression of at least one biomarker compared to baseline is indicative of a favorable response of the patient to the treatment.
  • Another aspect of the invention is a method of utilizing a biomarker in treatment of a patient.
  • An FGFR3 inhibitor may be administered and gene expression level of one or more biomarkers tested. Thereafter, the same or a different inhibitor may be administered in the treatment.
  • Yet another aspect of the invention is a method of treatment for multiple myeloma.
  • the method utilizes an agent that alters the level of expression of one or more of the identified biomarkers.
  • a method of adjusting a dosage amount of an inhibitor of FGFR3 for treatment of a cell proliferative disorder in a patient comprises administering an initial amount of the inhibitor of FGFR3 to the patient, monitoring gene expression on a sample from the patient for at least one of the identified biomarkers and adjusting the dosage amount for subsequent administration to the patient, depending on the level of expression of the biomarker or biomarkers that has occurred upon administration of the initial amount.
  • a further embodiment of the invention is a method of utilizing a biomarker to identify an FGFR3 inhibitory compound for potential treatment or further development.
  • the invention is an example of translational medicine at work, wherein patients may be treated selectively based on their particular genetic profile.
  • a cell includes a plurality of cells, including mixtures thereof.
  • polynucleotide and “oligonucleotide” are used interchangeably and refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides or analogs thereof. Polynucleotides can have any three-dimensional structure and may perform any function, known or unknown.
  • polynucleotides a gene or gene fragment (for example, a probe, primer, EST or SAGE tag), exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers.
  • a polynucleotide can comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs.
  • modifications to the nucleotide structure can be imparted before or after assembly of the polymer.
  • the sequence of nucleotides can be interrupted by non-nucleotide components.
  • a polynucleotide can be further modified after polymerization, such as by conjugation with a labeling component.
  • the term also refers to both double- and single-stranded molecules. Unless otherwise specified or required, any embodiment of this invention that is a polynucleotide encompasses both the double-stranded form and each of two complementary single-stranded forms known or predicted to make up the double-stranded form.
  • a polynucleotide is composed of a specific sequence of four nucleotide bases: adenine (A); cytosine (C); guanine (G); thymine (T); and uracil (U) for guanine when the polynucleotide is RNA.
  • A adenine
  • C cytosine
  • G guanine
  • T thymine
  • U uracil
  • polynucleotide sequence is the alphabetical representation of a polynucleotide molecule. This alphabetical representation can be input into databases in a computer having a central processing unit and used for bioinformatics applications such as functional genomics and homology searching.
  • a “gene” refers to a polynucleotide containing at least one open reading frame (ORE) that is capable of encoding a particular polypeptide or protein after being transcribed and translated.
  • a polynucleotide sequence may be used to identify larger fragments or full-length coding sequences of the gene with which they are associated. Methods of isolating larger fragment sequences are known to those of skill in the art.
  • a “gene product” or alternatively a “gene expression product” refers to the amino acid (e.g., peptide or polypeptide) generated when a gene is transcribed and translated.
  • polypeptide is used interchangeably with the term “protein” and in its broadest sense refers to a compound of two or more subunit amino acids, amino acid analogs, or peptidomimetics.
  • the subunits may be linked by peptide bonds. In another embodiment, the subunit may be linked by other bonds, e.g., ester, ether, etc.
  • amino acid refers to either natural and/or unnatural or synthetic amino acids, and both the D and L optical isomers, amino acid analogs, and peptidomimetics.
  • a peptide of three or more amino acids is commonly called an oligopeptide if the peptide chain is short. If the peptide chain is long, the peptide is commonly called a polypeptide or a protein.
  • compositions and methods comprising excluding other elements of any essential significance to the combination.
  • a composition consisting essentially of elements as listed would not exclude trace contaminants from the isolation and purification method and pharmaceutically acceptable carriers, such as phosphate buffered saline, preservatives and the like.
  • Consisting of shall mean excluding more than trace elements of other ingredients and substantial method steps of this invention. Embodiments defined by each of these transition terms are within the scope of this invention.
  • isolated means separated from constituents, cellular and otherwise, in which the polynucleotide, peptide, polypeptide, protein, antibody or fragments) thereof, are normally associated within nature.
  • an isolated polynucleotide is separated from the 3′ and 5′ contiguous nucleotides with which it is normally associated within its native or natural environment, e.g., on the chromosome.
  • a non-naturally occurring polynucleotide, peptide, polypeptide, protein, antibody, or fragment(s) thereof does not require “isolation” to distinguish it from its naturally occurring counterpart.
  • a “concentrated”, “separated” or “diluted” polynucleotide, peptide, polypeptide, protein, antibody or fragment(s) thereof is distinguishable from its naturally occurring counterpart in that the concentration or number of molecules per volume is greater in a “concentrated” version or less than in a “separated” version than that of its naturally occurring counterpart.
  • a non-naturally occurring polynucleotide is provided as a separate embodiment from the isolated naturally occurring polynucleotide.
  • a protein produced in a bacterial cell is provided as a separate embodiment from the naturally occurring protein isolated from a eukaryotic cell in which it is produced in nature.
  • a “probe” when used in the context of polynucleotide manipulation refers to an oligonucleotide that is provided as a reagent to detect a target potentially present in a sample of interest by hybridizing with the target.
  • a probe will comprise a label or a means by which a label can be attached, either before or subsequent to the hybridization reaction.
  • Suitable labels include, but are not limited to radioisotopes, fluorochromes, chemiluminescent compounds, dyes, and proteins, including enzymes.
  • a “primer” is a short polynucleotide, generally with a free 3′-OH group that binds to a target or “template” potentially present in a sample of interest by hybridizing with the target, and thereafter promoting polymerization of a polynucleotide complementary to the target.
  • a “polymerase chain reaction” (“PCR”) is a reaction in which replicate copies are made of a target polynucleotide using a “pair of primers” or a “set of primers” consisting of an “upstream” and a “downstream” primer, and a catalyst of polymerization, such as a DNA polymerase, and typically a thermally-stable polymerase enzyme.
  • PCR A PRACTICAL APPROACH
  • All processes of producing replicate copies of a polynucleotide, such as PCR or gene cloning, are collectively referred to herein as “replication.”
  • a primer can also be used as a probe in hybridization reactions, such as Southern or Northern blot analyses. Sambrook et al., supra.
  • expression refers to the process by which polynucleotides are transcribed into mRNA and/or the process by which the transcribed mRNA is subsequently translated into peptides, polypeptides or proteins. If the polynucleotide is derived from genomic DNA, expression may include splicing of the mRNA in a eukaryotic cell. “Differentially expressed” as applied to a gene, refers to the differential production of the mRNA transcribed and/or translated from the gene or the protein product encoded by the gene. A differentially expressed gene may be overexpressed or underexpressed as compared to the expression level of a normal or control cell.
  • overpression generally is at least 1.25 fold or, alternatively, at least 1.5 fold or, alternatively, at least 2 fold expression, or alternatively, at least 4 fold expression over that detected in a normal or healthy counterpart cell or tissue.
  • the term “differentially expressed” also refers to nucleotide sequences in a cell or tissue which are expressed where silent in a control cell or not expressed where expressed in a control cell.
  • a high expression level of the gene may occur because of over expression of the gene or an increase in gene copy number.
  • the gene may also be translated into more protein because of deregulation of a negative regulator.
  • a “gene expression profile” refers to a pattern of expression of a set of genes that recurs in multiple samples and reflects a property shared by those samples, such as tissue type, response to a particular treatment, or activation of a particular biological process or pathway in the cells. Furthermore, a gene expression profile differentiates between samples that share that common property and those that do not with better accuracy than would likely be achieved by assigning the samples to the two groups at random. A gene expression profile may be used to predict whether samples of unknown status share that common property or not.
  • database denotes a set of stored data that represent a collection of sequences, which in turn represent a collection of biological reference materials.
  • cDNAs refers to complementary DNA, i.e. mRNA molecules present in a cell or organism made into cDNA with an enzyme such as reverse transcriptase.
  • a “cDNA library” is a collection of all of the mRNA molecules present in a cell or organism, all turned into cDNA molecules with the enzyme reverse transcriptase, then inserted into “vectors” (other DNA molecules that can continue to replicate after addition of foreign DNA).
  • vectors for libraries include bacteriophage (also known as “phage”), viruses that infect bacteria, for example, lambda phage. The library can then be probed for the specific cDNA (and thus mRNA) of interest.
  • solid phase support or “solid support”, used interchangeably, is not limited to a specific type of support. Rather a large number of supports are available and are known to one of ordinary skill in the art.
  • Solid phase supports include silica gels, resins, derivatized plastic films, glass beads, cotton, plastic beads, alumina gels, microarrays, and chips.
  • solid support also includes synthetic antigen-presenting matrices, cells, and liposomes. A suitable solid phase support may be selected on the basis of desired end use and suitability for various protocols.
  • solid phase support may refer to resins such as polystyrene (e.g., PAM-resin obtained from Bachem Inc., Peninsula Laboratories, etc.), POLYHIPE® resin (obtained from Aminotech, Canada), polyamide resin (obtained from Peninsula Laboratories), polystyrene resin grafted with polyethylene glycol (TentaGel®, Rapp Polymere, Tubingen, Germany), or polydimethylacrylamide resin (obtained from Milligen/Biosearch, Calif.).
  • polystyrene e.g., PAM-resin obtained from Bachem Inc., Peninsula Laboratories, etc.
  • POLYHIPE® resin obtained from Aminotech, Canada
  • polyamide resin obtained from Peninsula Laboratories
  • polystyrene resin grafted with polyethylene glycol TeentaGel®, Rapp Polymere, Tubingen, Germany
  • polydimethylacrylamide resin obtained from Milligen/Biosearch, Calif.
  • a polynucleotide also can be attached to a solid support for use in high throughput screening assays.
  • PCT WO 97/10365 discloses the construction of high density oligonucleotide chips. See also, U.S. Pat. Nos. 5,405,783; 5,412,087; and 5,445,934.
  • the probes are synthesized on a derivatized glass surface to form chip arrays.
  • Photoprotected nucleoside phosphoramidites are coupled to the glass surface, selectively deprotected by photolysis through a photolithographic mask and reacted with a second protected nucleoside phosphoramidite. The coupling/deprotection process is repeated until the desired probe is complete.
  • transcriptional activity may be assessed by measuring levels of messenger RNA using a gene chip such as the Affymetrix HG-U133-Plus-2 GeneChips. High-throughput, real-time quanititation of RNA (of hundreds of genes simultaneously) thus becomes possible in a reproducible system.
  • Hybridization refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues.
  • the hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding or in any other sequence-specific mariner.
  • the complex may comprise two strands forming a duplex structure, three or more strands forming a multi-stranded complex, a single self-hybridizing strand, or any combination of these.
  • a hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PCR reaction or the enzymatic cleavage of a polynucleotide by a ribozyme.
  • Hybridization reactions can be performed under conditions of different “stringency”. In general, a low stringency hybridization reaction is carried out at about 40° C. in 10 ⁇ SSC or a solution of equivalent ionic strength/temperature. A moderate stringency hybridization is typically performed at about 50° C. in 6 ⁇ SSC, and a high stringency hybridization reaction is generally performed at about 60° C. in 1 ⁇ SSC.
  • a double-stranded polynucleotide can be “complementary” or “homologous” to another polynucleotide, if hybridization can occur between one of the strands of the first polynucleotide and the second.
  • “Complementarity” or “homology” is quantifiable in terms of the proportion of bases in opposing strands that are expected to form hydrogen bonding with each other, according to generally accepted base-pairing rules.
  • a polynucleotide or polynucleotide region has a certain percentage (for example, 80%, 85%, 90%, or 95%) of “sequence identity” to another sequence means that, when aligned, that percentage of bases (or amino acids) are the same in comparing the two sequences.
  • This alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel et al., eds., 1987) Supplement 30, section 7.7.18, Table 7.7.1.
  • default parameters are used for alignment.
  • a preferred alignment program is BLAST, using default parameters.
  • cell proliferative disorders shall include dysregulation of normal physiological function characterized by abnormal cell growth and/or division or loss of function.
  • Examples of “cell proliferative disorders” includes but is not limited to hyperplasia, neoplasia, metaplasia, and various autoimmune disorders, e.g., those characterized by the dysregulation of T cell apoptosis.
  • Hyperplasia is a form of controlled cell proliferation involving an increase in cell number in a tissue or organ, without significant alteration in structure or function.
  • Metaplasia is a form of controlled cell growth in which one type of fully differentiated cell substitutes for another type of differentiated cell. Metaplasia can occur in epithelial or connective tissue cells. Atypical metaplasia involves a somewhat disorderly metaplastic epithelium.
  • Neoplastic cells refer to cells which exhibit relatively autonomous growth, so that they exhibit an aberrant growth phenotype characterized by a significant loss of control of cell proliferation (i.e., de-regulated cell division).
  • Neoplastic cells can be malignant or benign.
  • a metastatic cell or tissue means that the cell can invade and destroy neighboring body structures.
  • “Suppressing” tumor growth indicates a growth state that is curtailed when compared to growth without contact with educated, antigen-specific immune effector cells.
  • Tumor cell growth can be assessed by any means known in the art, including, but not limited to, measuring tumor size, determining whether tumor cells are proliferating using a 3 H-thymidine incorporation assay or counting tumor cells.
  • “Suppressing” tumor cell growth means any or all of the following states: slowing, delaying and stopping tumor growth, as well as tumor shrinkage.
  • composition is also intended to encompass a combination of active agent and another carrier, e.g., compound or composition, inert (for example, a detectable agent or label) or active, such as an adjuvant, diluent, binder, stabilizer, buffers, salts, lipophilic solvents, preservative, adjuvant or the like.
  • carrier e.g., compound or composition
  • inert for example, a detectable agent or label
  • active such as an adjuvant, diluent, binder, stabilizer, buffers, salts, lipophilic solvents, preservative, adjuvant or the like.
  • Carriers also include pharmaceutical excipients and additives proteins, peptides, amino acids, lipids, and carbohydrates (e.g., sugars, including monosaccharides, di-, tri-, tetra-, and oligosaccharides; derivatized sugars such as alditols, aldonic acids, esterified sugars and the like; and polysaccharides or sugar polymers), which can be present singly or in combination, comprising alone or in combination 1-99.99% by weight or volume.
  • Exemplary protein excipients include serum albumin such as human serum albumin (HSA), recombinant human albumin (rHA), gelatin, casein, and the like.
  • amino acid/antibody components which can also function in a buffering capacity, include alanine, glycine, arginine, betaine, histidine, glutamic acid, aspartic acid, cysteine, lysine, leucine, isoleucine, valine, methionine, phenylalanine, aspartame, and the like.
  • Carbohydrate excipients are also intended within the scope of this invention, examples of which include but are not limited to monosaccharides such as fructose, maltose, galactose, glucose, D-mannose, sorbose, and the like; disaccharides, such as lactose, sucrose, trehalose, cellobiose, and the like; polysaccharides, such as raffinose, melezitose, maltodextrins, dextrans, starches, and the like; and alditols, such as mannitol, xylitol, maltitol, lactitol, xylitol sorbitol (glucitol) and myoinositol.
  • monosaccharides such as fructose, maltose, galactose, glucose, D-mannose, sorbose, and the like
  • disaccharides such as lactose, sucrose
  • the term carrier further includes a buffer or a pH adjusting agent; typically, the buffer is a salt prepared from an organic acid or base.
  • Representative buffers include organic acid salts such as salts of citric acid, ascorbic acid, gluconic acid, carbonic acid, tartaric acid, succinic acid, acetic acid, or phthalic acid; Tris, tromethamine hydrochloride, or phosphate buffers.
  • Additional carriers include polymeric excipients/additives such as polyvinylpyrrolidones, ficolls (a polymeric sugar), dextrates (e.g., cyclodextrins, such as 2-hydroxypropyl-.quadrature.-cyclodextrin), polyethylene glycols, flavoring agents, antimicrobial agents, sweeteners, antioxidants, antistatic agents, surfactants (e.g., polysorbates such as “TWEEN 20” and “TWEEN 80”), lipids (e.g., phospholipids, fatty acids), steroids (e.g., cholesterol), and chelating agents (e.g., EDTA).
  • polymeric excipients/additives such as polyvinylpyrrolidones, ficolls (a polymeric sugar), dextrates (e.g., cyclodextrins, such as 2-hydroxypropyl-.quadrature.-cyclodextrin), polyethylene glycols, flavor
  • the term “pharmaceutically acceptable carrier” encompasses any of the standard pharmaceutical carriers, such as a phosphate buffered saline solution, water, and emulsions, such as an oil/water or water/oil emulsion, and various types of wetting agents.
  • compositions also can include stabilizers and preservatives and any of the above noted carriers with the additional provisio that they be acceptable for use in vivo.
  • carriers for examples of carriers, stabilizers and adjuvants, see Martin REMINGTON'S PHARM. SCI., 15th Ed. (Mack Publ. Co., Easton (1975) and Williams & Williams, (1995), and in the “PHYSICIAN'S DESK REFERENCE”, 52 nd ed., Medical Economics, Montvale, N.J. (1998).
  • an “effective amount” is an amount sufficient to effect beneficial or desired results.
  • An effective amount can be administered in one or more administrations, applications or dosages.
  • a “subject,” “individual” or “patient” is used interchangeably herein, which refers to a vertebrate, preferably a mammal, more preferably a human. Mammals include, but are not limited to, murines, simians, humans, farm animals, sport animals, and pets.
  • FGFR3 is the acronym for fibroblast growth factor receptor 3.
  • the fibroblast growth factors are a family of polypeptide growth factors involved in a variety of activities, including mitogenesis, angiogenesis, and wound healing. They contain an extracellular domain with either 2 or 3 immunoglobulin (Ig)-like domains, a transmembrane domain, and a cytoplasmic tyrosine kinase domain.
  • Ig immunoglobulin
  • FGFR3 was cloned by Keegan et al., PNAS, 88:1095-1099 (1991). Inhibition of activated FGFR3 in t(4; 14) multiple myeloma patients is thought to lead to apoptosis. Trudel, et al., Blood, 105(7):2941-2948 (2005); Grand, et al., Leukemia, 18:962-966 (2004).
  • an “inhibitor” of FGFR3 as used herein binds or blocks or diminishes the effect of the FGFR3.
  • Examples include, but are not limited to CHIR-258 and related compounds, SU-5402, PD-173074, and siRNA.
  • a “biomarker” is a distinctive indicator or specific feature or characteristic of a biological process or event. As used herein, a biomarker is a gene. A biomarker may be especially useful for measuring the progress of a disease or the response to a given treatment. In addition to assessing prognosis, in some instances, it may be used to diagnose an illness or screen for patients within a category, such as those most likely to respond to a certain type of treatment. A biomarker may also be useful in guiding the development or administration of an agent for treatment of a disease.
  • the invention provides methods of identifying patients suitable for treatment and methods of monitoring response in patients receiving treatment. Also provided are methods of treatment and methods of adjusting dosage amounts by utilizing the biomarkers disclosed herein. Methods of identifying the appropriate inhibitory compound are also within the scope of the invention.
  • the present invention also provides a screen for various agents and methods that may supplement or replace the anti-FGFR3 therapy known in the art.
  • the agent alone or in combination with another agent or therapy method, is provided to the patient. After administration, a sample from the patient is screened for expression of one or more biomarkers identified herein and then compared to a pre-determined baseline.
  • Kits containing an FGFR3 inhibitor and instructions necessary to perform a method of the invention also are within the scope of the invention.
  • the presence or absence of gene expression or the level or amount of gene expression of one or more of the biomarkers identified herein may be used to guide treatment decisions and measure responsiveness of the patient to a given type of treatment. For example, detection of the presence or lack thereof of gene expression or alteration of the level of gene expression compared to a predetermined baseline of one or more of the biomarkers identified in Tables I-V provides information regarding whether a patient may be a suitable candidate for treatment by CHIR-258 or another FGFR3 inhibitor.
  • biomarkers may be of particular interest: CCL3, LOC150271, CD48, DUSP4, ITGB7, DUSP6, ANXA9, CR2, AL531683, ZNF589, AW274468, FRMD3, LTB, and WDR42A.
  • gene expression can be measured by detecting the presence or absence, or presence and/or absolute or relative quantity of a gene expression product (e.g., RNA, mRNA, or the protein or polypeptide transcript) or the alteration in gene copy number.
  • altered expression is likely the result of an increase in copy number.
  • altered expression is likely the result of the loss of function of another gene such as a tumor suppressor or other negative regulator.
  • expression is altered by the “turning on” of an enhancer. Accordingly, the specific method used to detect altered expression, as compared to the control or baseline, may be different and dependent on the particular biomarker selected.
  • the method requires analysis of gene expression of one or more predetermined biomarkers by more than one method, e.g., by use of immunohistochemical and molecular techniques such as a gene chip or array.
  • Table I is a list of biomarkers whose expression is indicative of activity related to FGFR3 inhibition.
  • Table II is a preferred subset of Table I according to one aspect of the invention, listing biomarkers generally having a higher level of alteration of gene expression compared to baseline in response to FGFR3 inhibition.
  • Table III is more preferred subset of Table I according to one aspect of the invention, listing biomarkers generally having the highest level of alteration of gene expression compared to so baseline in response to FGFR3 inhibition.
  • Table IV is a preferred subset of Table I according to a second aspect of the invention, listing biomarkers generally exhibiting the strongest correlation of gene expression in response to FGFR3 inhibition by the preferred compound, CHIR-258.
  • Table V is a more preferred subset of Table I according to a second aspect of the invention, listing biomarkers generally exhibiting the strongest correlation of gene expression in response to FGFR3 inhibition by the preferred compound, CHTR-258, in preference to either SU-5402 or PD-173074.
  • EDG2 endothelial differentiation lysophosphatidic acid G- protein-coupled receptor, 2 81. 64946 CENPH centromere protein H 82. 157570 ESCO2 establishment of cohesion 1 homolog 2 ( S. cerevisiae ) 83. 389835 FAM72A family with sequence similarity 72, member A 84. 144455 E2F7 E2F transcription factor 7 85. 51512 GTSE1 G-2 and S-phase expressed 1 86. 7298 TYMS thymidylate synthetase 87. 7374 UNG uracil-DNA glycosylase 88. 5578 PRKCA protein kinase C, alpha 89.
  • RHAMM hyaluronan-mediated motility receptor
  • 10276 NET1 neuroepithelial cell transforming gene 1 127. 29028 ATAD2 ATPase family, AAA domain containing 2 128. 1062 CENPE centromere protein E, 312 kDa 129. 1491 CTH cystathionase (cystathionine gamma-lyase) 130. 10615 SPAG5 sperm associated antigen 5 131. 64581 CLEC7A C-type lectin domain family 7, member A 132. 10592 SMC2L1 SMC2 structural maintenance of chromosomes 2- like 1 (yeast) 133. 332 BIRC5 baculoviral IAP repeat-containing 5 (survivin) 134.
  • BCL11B B-cell CLL/lymphoma 11B (zinc finger protein) 214. 26095 PTPN20 protein tyrosine phosphatase, non-receptor type 20 215. 23590 TPRT trans-prenyltransferase 216. 387882 LOC387882 hypothetical protein 217. 51232 CRIM1 cysteine-rich motor neuron 1 218. 801 CALM1 calmodulin 1 (phosphorylase kinase, delta) 219. 55964 SEPT3 septin 3 220. 493861 EID3 E1A-like inhibitor of differentiation 3 221. 29980 DONSON downstream neighbor of SON 222.
  • ENO2 enolase 2 (gamma, neuronal) 286.
  • CTNNAL1 catenin (cadherin-associated protein), alpha-like 1 287. 5880 RAC2 ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) 288.
  • RUNX3 runt-related transcription factor 3 289. 10950 BTG3 BTG family, member 3 290. 81539 SLC38A1 solute carrier family 38, member 1 291.
  • TCF3 transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47) 353.
  • 81611 ANP32E acidic (leucine-rich) nuclear phosphoprotein 32 family, member E 358.
  • ANKRD32 ankyrin repeat domain 32 361. 6999 TDO2 tryptophan 2,3-dioxygenase 362.
  • PRTFDC1 phosphoribosyl transferase domain containing 1 392.
  • SHMT2 serine hydroxymethyltransferase 2 (mitochondrial) 393.
  • BCAT1 branched chain aminotransferase 1, cytosolic 395.
  • 8836 GGH gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase) 396.
  • CD44 CD44 antigen (homing function and Indian blood group system) 406. 81930 KIF18A kinesin family member 18A 407. 64116 SLC39A8 solute carrier family 39 (zinc transporter), member 8 408. 26586 CKAP2 cytoskeleton associated protein 2 409. 51144 HSD17B12 hydroxysteroid (17-beta) dehydrogenase 12 410. 51002 CGI-121 CGI-121 protein 411. 9126 CSPG6 chondroitin sulfate proteoglycan 6 (bamacan) 412. 79154 MGC4172 short-chain dehydrogenase/reductase 413.
  • ADAMTS5 a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2) 414. 84803 MGC11324 hypothetical protein MGC11324 415. 4082 MARCKS myristoylated alanine-rich protein kinase C substrate 416. 4086 SMAD1 SMAD, mothers against DPP homolog 1 ( Drosophila ) 417. 9446 GSTO1 glutathione S-transferase omega 1 418. 23636 NUP62 nucleoporin 62 kDa 419. 81839 VANGL1 vang-like 1 (van gogh, Drosophila ) 420.
  • LSM4 LSM4 homolog U6 small nuclear RNA associated ( S. cerevisiae ) 457. 3939 LDHA lactate dehydrogenase A 458. 57552 AADACL1 arylacetamide deacetylase-like 1 459. 9184 BUB3 BUB3 budding uninhibited by benzimidazoles 3 homolog (yeast) 460. 657 BMPR1A bone morphogenetic protein receptor, type IA 461. 5631 PRPS1 phosphoribosyl pyrophosphate synthetase 1 462. 204 AK2 adenylate kinase 2 463.
  • nudix nudix (nucleoside diphosphate linked moiety X)-type motif 15 464. 10265 IRX5 iroquois homeobox protein 5 465. 4640 MYO1A myosin IA 466. 79180 EFHD2 EF hand domain family, member D2 467. 4076 M11S1 membrane component, chromosome 11, surface marker 1 468. 55276 PGM2 phosphoglucomutase 2 469. 83857 ARG99 ARG99 protein 470. 116448 OLIG1 oligodendrocyte transcription factor 1 471. 5696 PSMB8 proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7) 472.
  • TKT transketolase (Wernicke-Korsakoff syndrome) 482. 51174 TUBD1 tubulin, delta 1 483. 23255 KIAA0802 KIAA0802 484. 54149 C21orf91 chromosome 21 open reading frame 91 485. 2271 FH fumarate hydratase 486. 55076 TMEM45A transmembrane protein 45A 487. 10436 C2F C2f protein 488. 8553 BHLHB2 basic helix-loop-helix domain containing, class B, 2 489. 10409 BASP1 brain abundant, membrane attached signal protein 1 490. 22856 CHSY1 carbohydrate (chondroitin) synthase 1 491.
  • HMGN1 high-mobility group nucleosome binding domain 1 493. 961 CD47 CD47 antigen (Rh-related antigen, integrin- associated signal transducer) 494. 79038 ZFYVE21 zinc finger, FYVE domain containing 21 495. 7291 TWIST1 twist homolog 1 (acrocephalosyndactyly 3; Saethre- Chotzen syndrome) ( Drosophila ) 496. 9738 CP110 CP110 protein 497. 10625 IVNS1ABP influenza virus NS1A binding protein 498.
  • SFRS1 splicing factor 6426 SFRS1 splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) 561. 81831 NETO2 neuropilin (NRP) and tolloid (TLL)-like 2 562. 56888 KCMF1 potassium channel modulatory factor 1 563. 9221 NOLC1 nucleolar and coiled-body phosphoprotein 1 564. 79366 NSBP1 nucleosomal binding protein 1 565. 51729 WBP11 WW domain binding protein 11 566. 84444 DOT1L DOT1-like, histone H3 methyltransferase ( S. cerevisiae ) 567. 80218 MAK3 Mak3 homolog ( S.
  • SR140 U2-associated SR140 protein 620. 6434 SFRS10 splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila ) 621. 7975 MAFK v-maf musculoaponeurotic fibrosarcoma oncogene homolog K (avian) 622. 3187 HNRPH1 heterogeneous nuclear ribonucleoprotein H1 (H) 623. 94239 H2AFV H2A histone family, member V 624. 54913 RPP25 ribonuclease P 25 kDa subunit 625.
  • EEF1E1 eukaryotic translation elongation factor 1 epsilon 1 626. 5471 PPAT phosphoribosyl pyrophosphate amidotransferase 627. 340252 ZNF680 zinc finger protein 680 628. 1021 CDK6 cyclin-dependent kinase 6 629. 10560 SLC19A2 solute carrier family 19 (thiamine transporter), member 2 630. 4201 MEA1 male-enhanced antigen 1 631. 440145 LOC440145 similar to RIKEN cDNA 2410129H14 632. 3843 RANBP5 RAN binding protein 5 633. 3298 HSF2 heat shock transcription factor 2 634.
  • TMEM46 transmembrane protein 46 635. 27347 STK39 serine threonine kinase 39 (STE20/SPS1 homolog, yeast) 636. 6256 RXRA retinoid X receptor, alpha 637. 6637 SNRPG small nuclear ribonucleoprotein polypeptide G 638. 22800 RRAS2 related RAS viral (r-ras) oncogene homolog 2 639. 91694 FLJ23749 hypothetical protein FLJ23749 640. 22823 MTF2 metal response element binding transcription factor 2 641. 51184 MGC14560 protein x 0004 642. 10856 RUVBL2 RuvB-like 2 ( E. coli ) 643.
  • MGC40405 hypothetical protein MGC40405 736.
  • MTHFD1 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase 739.
  • MESDC1 mesoderm development candidate 1 757.
  • LARP1 La ribonucleoprotein domain family member 1 796. 5778 PTPN7 protein tyrosine phosphatase, non-receptor type 7 797. 100 ADA adenosine deaminase 798. 2821 GPI glucose phosphate isomerase 799. 9697 TRAM2 translocation associated membrane protein 2 800. 54927 CHCHD3 coiled-coil-helix-coiled-coil-helix domain containing 3 801. 58478 MASA E-1 enzyme 802. 6322 SCML1 sex comb on midleg-like 1 ( Drosophila ) 803.
  • SLC25A5 solute carrier family 25 mitochondrial carrier; adenine nucleotide translocator, member 5 804.
  • PGRMC1 progesterone receptor membrane component 1 805.
  • CBR3 carbonyl reductase 3 808.
  • 51096 WDR50 WD repeat domain 50 809. 253558 LYCAT lysocardiolipin acyltransferase 810. 79053 ALG8 asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase) 811.
  • 6731 SRP72 signal recognition particle 72 kDa 835.
  • 2273 FHL1 four and a half LIM domains 1 837.
  • SII transcription elongation factor A
  • NME7 non-metastatic cells 7 protein expressed in (nucleoside-diphosphate kinase) 863. 8887 TAX1BP1 Tax1 (human T-cell leukemia virus type I) binding protein 1 864. 5445 PON2 paraoxonase 2 865. 81889 FAHD1 fumarylacetoacetate hydrolase domain containing 1 866. 694 BTG1 B-cell translocation gene 1, anti-proliferative 867. 29058 C20orf30 chromosome 20 open reading frame 30 868. 2752 GLUL glutamate-ammonia ligase (glutamine synthase) 869. 79717 FLJ11838 hypothetical protein FLJ11838 870.
  • 6926 TBX3 T-box 3 (ulnar mammary syndrome) 880. 51614 SDBCAG84 serologically defined breast cancer antigen 84 881. 9520 NPEPPS aminopeptidase puromycin sensitive 882. 51065 RPS27L ribosomal protein S27-like 883. 10116 FEM1B fem-1 homolog b ( C. elegans ) 884. 10521 DDX17 DEAD (Asp-Glu-Ala-Asp) box polypeptide 17 885. 81557 MAGED4 melanoma antigen family D, 4 886. 10133 OPTN optineurin 887.
  • ANKRD29 ankyrin repeat domain 29 935 3757 KCNH2 potassium voltage-gated channel, subfamily H (eag- related), member 2 936. 116442 RAB39B RAB39B, member RAS oncogene family 937. 10972 TMP21 transmembrane trafficking protein 938. 57798 GATAD1 GATA zinc finger domain containing 1 939. 1314 COPA coatomer protein complex, subunit alpha 940. 2581 GALC galactosylceramidase (Krabbe disease) 941. 91452 ACBD5 acyl-Coenzyme A binding domain containing 5 942. 8879 SGPL1 sphingosine-1-phosphate lyase 1 943.
  • SCARB1 scavenger receptor class B member 1 1012. 1519 CTSO cathepsin O 1013. 51136 LOC51136 PTD016 protein 1014. 3428 IFI16 interferon, gamma-inducible protein 16 1015. 9516 LITAF lipopolysaccharide-induced TNF factor 1016. 3123 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 1017. 1389 CREBL2 cAMP responsive element binding protein-like 2 1018. 5027 P2RX7 purinergic receptor P2X, ligand-gated ion channel, 7 1019. 6782 STCH stress 70 protein chaperone, microsome-associated, 60 kDa 1020.
  • CTBS chitobiase di-N-acetyl- 1028. 4601 MXI1 MAX interactor 1 1029. 1365 CLDN3 claudin 3 1030. 81622 UNC93B1 unc-93 homolog B1 ( C. elegans ) 1031. 54664 FLJ11273 hypothetical protein FLJ11273 1032. 9993 DGCR2 DiGeorge syndrome critical region gene 2 1033. 57179 KIAA1191 KIAA1191 protein 1034. 55958 KLHL9 kelch-like 9 ( Drosophila ) 1035. 81671 TMEM49 transmembrane protein 49 1036. 9666 DZIP3 zinc finger DAZ interacting protein 3 1037.
  • 8804 CREG1 cellular repressor of E1A-stimulated genes 1 1101. 84181 CHD6 chromodomain helicase DNA binding protein 6 1102. 22871 NLGN1 neuroligin 1 1103. 659 BMPR2 bone morphogenetic protein receptor, type II (serine/threonine kinase) 1104.
  • TPP1 tripeptidyl peptidase I 1156. 5973 RENBP renin binding protein 1157. 7259 TSPYL1 TSPY-like 1 1158. 112770 C1orf85 chromosome 1 open reading frame 85 1159. 93953 ACRC acidic repeat containing 1160. 90634 CG018 hypothetical gene CG018 1161. 1030 CDKN2B cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4) 1162. 158158 RASEF RAS and EF hand domain containing 1163. 2824 GPM6B glycoprotein M6B 1164. 9706 ULK2 unc-51-like kinase 2 ( C. elegans ) 1165.
  • PLEKHA1 pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1 1215. 3727 JUND jun D proto-oncogene 1216. 85236 HIST1H2BK histone 1, H2bk 1217. 6513 SLC2A1 solute carrier family 2 (facilitated glucose transporter), member 1 1218. 155038 GIMAP8 GTPase, IMAP family member 8 1219. 3055 HCK hemopoietic cell kinase 1220. 6542 SLC7A2 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 1221. 8996 NOL3 nucleolar protein 3 (apoptosis repressor with CARD domain) 1222.
  • ARMCX3 armadillo repeat containing, X-linked 3 1271. 9388 LIPG lipase, endothelial 1272. 27250 PDCD4 programmed cell death 4 (neoplastic transformation inhibitor) 1273. 6302 SAS sarcoma amplified sequence 1274. 83937 RASSF4 Ras association (RalGDS/AF-6) domain family 4 1275. 388677 NOTCH2NL Notch homolog 2 ( Drosophila ) N-terminal like 1276. 23646 PLD3 phospholipase D family, member 3 1277. 23643 LY96 lymphocyte antigen 96 1278. 9855 FARP2 FERM, RhoGEF and pleckstrin domain protein 2 1279.
  • MLF1IP MLF1 interacting protein 70 6790 STK6 serine/threonine kinase 6 71. 3925 STMN1 stathmin 1/oncoprotein 18 72. 11004 KIF2C kinesin family member 2C 73. 10276 NET1 neuroepithelial cell transforming gene 1 74. 3015 H2AFZ H2A histone family, member Z 75. 891 CCNB1 cyclin B1 76. 389835 FAAM72A family with sequence similarity 72, member A 77. 5111 OCNA proliferating cell nuclear antigen 78. 9837 PSF1 DNA replication complex GINS protein PSF1 79. 3148 HMGB2 high-mobility group box 2 80.
  • HCAP-G chromosome condensation protein G 145. 11151 CORO1A coronin, actin binding protein, 1A 146. 203068 TUBB tubulin, beta polypeptide 147. 10926 ASK activator of S phase kinase 148. 11073 TOPBP1 topoisomerase (DNA) II binding protein 1 149. 90417 C15orf23 chromosome 15 open reading frame 23 150. 9493 KIF23 kinesin family member 23 151. 387882 LOC387882 hypothetical protein 152. 23234 DNAJC9 DnaJ (Hsp40) homolog, subfamily C, member 9 153. 2146 EZH2 enhancer of zeste homolog 2 (Drosophila) 154.
  • PSAP prosaposin variant Gaucher disease and variant metachromatic leukodystrophy 239.
  • PLD3 phospholipase D family member 3 271. 51566 ARMCX3 armadillo repeat containing, X-linked 3 272. 58476 TP53INP2 tumor protein p53 inducible nuclear protein 2 273. 29994 BAZ2B bromodomain adjacent to zinc finger domain, 2B 274. 283131 TncRNA trophoblast-derived noncoding RNA 275. 4189 DNAJB9 DnaJ (Hsp40) homolog, subfamily B, member 9 276. 9123 SLC16A3 solute carrier family 16 (monocarboxylic acid transporters), member 3 277.
  • EGLN3 egl nine homolog 3 ( C. elegans ) 319. 22871 NLGN1 neuroligin 1 320. 8804 CREG1 cellular repressor of E1A-stimulated genes 1 321. 401081 FLJ22763 hypothetical gene supported by AK026416 322. 25924 MYRIP myosin VIIA and Rab interacting protein 323. 91694 FLJ23749 hypothetical protein FLJ23749 324. 56155 TEX14 testis expressed sequence 14 325. 1349 COX7B cytochrome c oxidase subunit VIIb 326. 3695 ITGB7 integrin, beta 7 327.
  • SDC4 syndecan 4 (amphiglycan, ryudocan) 439.
  • 205 AK3L1 adenylate kinase 3-like 1 440.
  • 2026 ENO2 enolase 2 (gamma, neuronal) 442.
  • 23046 KIF21B kinesin family member 21B 443.
  • 60468 BACH2 BTB and CNC homology 1 basic leucine zipper transcription factor 2 444. 55013 FLJ20647 hypothetical protein FLJ20647 445.
  • ST6GALNAC3 ST6 alpha-N-acetyl-neuraminyl-2,3-beta- galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6- sialyltransferase 3 446.
  • TAF5 TAF5 RNA polymerase II TATA box binding protein (TBP)-associated factor, 100 kDa 451.
  • TBP TATA box binding protein
  • 23531 MMD monocyte to macrophage differentiation-associated 453.
  • 79621 FLJ11712 hypothetical protein FLJ11712 454.
  • PANK1 pantothenate kinase 1 456.
  • 6558 SLC12A2 solute carrier family 12 (sodium/potassium/chloride transporters), member 2 458.
  • PKP4 plakophilin 4 459. 116496 C1orf24 chromosome 1 open reading frame 24 460. 84314 MGC10744 hypothetical protein MGC10744 461. 54830 FLJ20130 hypothetical protein FLJ20130 462.
  • VANGL1 vang-like 1 van gogh, Drosophila
  • 9734 HDAC9 histone deacetylase 9 486. 51703 ACSL5 acyl-CoA synthetase long-chain family member 5 487. 10155 TRIM28 tripartite motif-containing 28 488. 54566 EPB41L4B erythrocyte membrane protein band 4.1 like 4B 489. 10019 LNK lymphocyte adaptor protein 490.
  • MARCKS myristoylated alanine-rich protein kinase C substrate 491. 23012 STK38L serine/threonine kinase 38 like 492.
  • 200894 ARL2L1 ADP-ribosylation factor-like 2-like 1 521. 10625 IVNS1ABP influenza virus NS1A binding protein 522. 10436 C2F C2f protein 523. 79038 ZFYVE21 zinc finger, FYVE domain containing 21 524. 7091 TLE24 transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila) 525. 7291 TWIST1 twist homolog 1 (acrocephalosyndactyly 3; Saethre- Chotzen syndrome) (Drosophila) 526. 87 ACTN1 actinin, alpha 1 527. 1736 DKC1 dyskeratosis congenita 1, dyskerin 528.
  • HIST2H2AA histone 2 H2aa 574. 10057 ABCC5 ATP-binding cassette, sub-family C (CFTR/MRP), member 5 575. 5274 SERPINI1 serine (or cyesteine) proteinase inhibitor, clade I (neuroserpin), member 1 576. 3358 HTRC2 5-hydroxytryptamine (serotonin) receptor 2C 577. 158158 RASEF RAS and EF hand domain containing 578. 304 ANXA2P2 annexin A2 pseudogene 2 579. 7259 TSPYL1 TSPY-like 1 580. 8878 SQSTM1 sequestosome 1 581.
  • GALNT2 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2) 597.
  • TIPARP TCDD-inducible poly(ADP-ribose) polymerase 598.
  • 57674 C17orf27 chromosome 17 open reading frame 27 599.
  • ACRC acidic repeat containing 601. 6990 TCTE1L t-complex-associated-testis-expressed 1-like 602. 571 BACH1 BTB and CNC homology 1, basic leucine zipper transcription factor 1 603.
  • PLEKHH2 pleckstrin homology domain containing, family H (with MyTH4 domain) member 2 626. 81930 KIF18A kinesin family member 18A 627. 11096 ADAMTS5 a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2) 628. 4148 MATN3 matrilin 3 629. 56121 PCDHB15 photocadherin beta 15 630. 57552 AADACL1 arylacetamide deacetylase-like 1 631. 64396 GMCL1L germ cell-less homolog 1 (Drosophila)-like 632.
  • ADAMTS5 a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2) 628. 4148 MATN3 matrilin 3 629. 56121 PCDHB15 photocadherin
  • SRGAP1 SLIT-ROBO Rho GTPase activating protein 1 714. 79695 GALNT12 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12) 715. 396 ARHGDIA Rho GDP dissociation inhibitor (GDI) alpha 716. 9208 LRRFIP1 leucine rich repeat (in FLII) interacting protein 1 717. 6453 ITSN1 intersectin 1 (SH3 domain protein) 718. 169200 DKFZp762C1112 hypothetical protein DKFZp762C1112 719.
  • E2F8 E2F transcription factor 8 56. 10112 KIF20A kinesin family member 20A 57. 54910 SEMA4C sema domain, immunoglobulin domain (Ig), transmemebrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C 58. 993 CDC25A cell division cycle 25A 59. 3683 ITGAL integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide) 60. 9355 LHX2 LIM homeobox 2 61. 5578 PRKCA protein kinase C, alpha 62. 157570 ESCO2 establishment of cohesion 1 homolog 2 ( S.
  • TRIB2 tribbles homolog 2 Drosophila 72. 1491 CTH cystathionase (cystathionine gamma-lyase) 73. 4281 MID1 midline 1 (Opitz/BBB syndrome) 74. 145482 ZADH1 zinc binding alcohol dehydrogenase, domain containing 1 75. 84858 ZNF503 zinc finger protein 503 76. 55723 ASF1B ASF1 anti-silencing function 1 homolog B ( S. cerevisiae ) 77. 1718 DHCR24 24-dehydrocholesterol reductase 78. 1847 DUSP5 dual specificity phosphatase 5 79.
  • MAPT microtubule-associated protein tau 133. 9099 USP2 ubiquitin specific protease 2 134. 5777 PTPN6 protein tyrosine phosphatase, non-receptor type 6 135. 59338 PLEKHA1 pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1 136. 1028 CDKN1C cyclin-dependent kinase inhibitor 1C (p57, Kip2)
  • MLF1IP MLF1 interacting protein 70 6790 STK6 serine/threonine kinase 6 71. 3925 STMN1 stathmin 1/oncoprotein 18 72. 11004 KIF2C kinesin family member 2C 73. 10276 NET1 neuroepithelial cell transforming gene 1 74. 3015 H2AFZ H2A histone family, member Z 75. 891 CCNB1 cyclin B1 76. 389835 FAM72A family with sequence similarity 72, member A 77. 5111 PCNA proliferating cell nuclear antigen 78. 9837 PSF1 DNA replication complex GINS protein PSF1 79. 3148 HMGB2 high-mobility group box 2 80.
  • HCAP-G chromosome condensation protein G 145. 11151 CORO1A coronin, actin binding protein, 1A 146. 203068 TUBB tubulin, beta polypeptide 147. 10926 ASK activator of S phase kinase 148. 11073 TOPBP1 topoisomerase (DNA) II binding protein 1 149. 90417 C15orf23 chromosome 15 open reading frame 23 150. 9493 KIF23 kinesin family member 23 151. 387882 LOC387882 hypothetical protein 152. 23234 DNAJC9 DnaJ (Hsp40) homolog, subfamily C, member 9 153. 2146 EZH2 enhancer of zeste homolog 2 ( Drosophila ) 154.
  • EXOSC8 exosome component 8 207. 2956 MSH6 mutS homolog 6 ( E. coli ) 208. 151246 SGOL2 shugoshin-like 2 ( S. pombe ) 209. 27346 MAC30 hypothetical protein MAC30 210. 5873 RAB27A RAB27A, member RAS oncogene family 211. 79596 C13orf7 chromosome 13 open reading frame 7 212. 10051 SMC4L1 SMC4 structural maintenance of chromosomes 4- like 1 (yeast) 213. 3336 HSPE1 heat shock 10 kDa protein 1 (chaperonin 10) 214.
  • RARRES3 retinoic acid receptor responder (tazarotene induced) 3 224. 400172 LOC400172 similar to KIAA1641 protein; melanoma-associated antigen; CLL-associated antigen KW-1 225. 55281 FLJ11000 hypothetical protein FLJ11000 226. 9783 RIMS3 regulating synaptic membrane exocytosis 3 227. 6480 ST6GAL1 ST6 beta-galactosamide alpha-2,6-sialyltranferase 1 228. 390 RND3 Rho family GTPase 3 229. 10765 JARID1B Jumonji, AT rich interactive domain 1B (RBP2-like) 230.
  • PLD3 phospholipase D family member 3 271. 51566 ARMCX3 armadillo repeat containing, X-linked 3 272. 58476 TP53INP2 tumor protein p53 inducible nuclear protein 2 273. 29994 BAZ2B bromodomain adjacent to zinc finger domain, 2B 274. 283131 TncRNA trophoblast-derived noncoding RNA 275. 4189 DNAJB9 DnaJ (Hsp40) homolog, subfamily B, member 9 276. 9123 SLC16A3 solute carrier family 16 (monocarboxylic acid transporters), member 3 277.
  • 961 CD47 CD47 antigen (Rh-related antigen, integrin- associated signal transducer) 357.
  • ATF3 activating transcription factor 3 380. 64778 FNDC3B fibronectin type III domain containing 3B 381. 347733 RP11-506K6.1 tubulin, beta polypeptide paralog 382. 9604 RNF14 ring finger protein 14 383. 7832 BTG2 BTG family, member 2 384. 120196 MGC34830 hypothetical protein MGC34830 385. 9910 RABGAP1L RAB GTPase activating protein 1-like 386. 55876 GSDML gasdermin-like 387. 1524 CX3CR1 chemokine (C—X3—C motif) receptor 1 388. 23015 GM88 88-kDa golgi protein 389.
  • 1604 DAF decay accelerating factor for complement (CD55, Cromer blood group system) 390. 114793 FMNL2 formin-like 2 391. 50640 IPLA2(GAMMA) intracellular membrane-associated calcium- independent phospholipase A2 gamma 392. 222166 Ells1 hypothetical protein Ells1 393. 10140 TOB1 transducer of ERBB2, 1 394. 1647 GADD45A growth arrest and DNA-damage-inducible, alpha 395. 25840 DKFZP586A0522 DKFZP586A0522 protein 396. 150759 LOC150759 hypothetical protein LOC150759 397.
  • SLC25A5 solute carrier family 25 mitochondrial carrier; adenine nucleotide translocator, member 5 572. 51096 WDR50 WD repeat domain 50 573. 79053 ALG8 asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase) 574. 84300 C6orf125 chromosome 6 open reading frame 125 575. 253461 ZBTB38 zinc finger and BTB domain containing 38 576. 29080 HSPC128 HSPC128 protein 577. 1622 DBI diazepam binding inhibitor (GABA receptor modulator, acyl-Coenzyme A binding protein) 578.
  • GABA receptor modulator acyl-Coenzyme A binding protein
  • HIST1H4C histone 1 H4c 10. 3725 JUN v-jun sarcoma virus 17 oncogene homolog (avian) 11. 384 ARG2 arginase, type II 12. 10129 13CDNA73 hypothetical protein CG003 13. 401081 FLJ22763 hypothetical gene supported by AK026416 14. 25924 MYRIP myosin VIIA and Rab interacting protein 15. 91694 FLJ23749 hypothetical protein FLJ23749 16. 56155 TEX14 testis expressed sequence 14 17. 1349 COX7B cytochrome c oxidase subunit VIIb 18. 1164 CKS2 CDC28 protein kinase regulatory subunit 2 19.
  • the gene expression of the biomarkers of Table I or any of its subsets, Tables II through V may be up- or down-regulated in response to the inhibition of FGFR3.
  • the detection of the presence of gene expression of one of the biomarkers may be sufficient to identify the patient for treatment or provide indication of a favorable response to treatment.
  • one may find identifying the most suitable patients for treatment for a particular cell proliferative disorder may best be accomplished by detecting an alteration in level of gene expression of two or more biomarkers or by a specific combination of biomarkers or even direction of alteration of gene expression.
  • a particular two of the biomarkers identified in Table I may be most correlated with a given condition and, thus, guide a certain treatment.
  • a ratio of the relative levels of gene expression of two particular biomarkers may be indicative of the suitability of a given treatment for a patient.
  • a particular condition may have a signature such as the up-regulation of one or more particular biomarker or biomarkers and/or the down-regulation of one or more other particular biomarker or biomarkers.
  • a baseline level may be established in several ways. For example, in a method of monitoring response of a patient to treatment, a sample may be obtained from the patient and tested for measurement of gene expression prior to introduction of an FGFR3 inhibitor to the patient. Thus, the profile of gene expression levels, if any, of biomarkers in a treatment-na ⁇ ve individual may serve as a baseline for that individual and later tests performed on samples obtained once treatment has begun may be compared to the individual's baseline.
  • a baseline may be established through creation of a guide that consolidates information on gene expression levels taken from a pool of healthy or treatment-na ⁇ ve individuals or even from an appropriate cell culture. Further, information on baseline levels of gene expression of particular biomarkers may be gathered from published sources or a gene database.
  • a sample is isolated from the patient after receipt of an amount of inhibitor of FGFR3, whether a therapeutically effective amount or a sub-therapeutically effective amount, which may be adequate for some purposes.
  • Cell or tissue samples used for this invention encompass body fluid, solid tissue samples, tissue cultures or cells derived therefrom and the progeny thereof, and sections or smears prepared from any of these sources, or any other samples that may contain genetic information. Measurement of the expression of the biomarkers is described in further detail below.
  • Some examples of small molecule inhibitors of FGFR3 include CHIR-258 (Chiron Corporation), SU-5402 (Pfizer, Inc.), and PD-173074 (Pfizer, Inc.).
  • 4-Amino-5-fluoro-3-[6-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]quinolin-2(1H)-one is a small molecule inhibitor of VEGF-RTK, PDGF-RTK and other receptor tyrosine kinases such as fibroblast growth factor receptor (FGF-RTK).
  • FGF-RTK fibroblast growth factor receptor
  • Such compounds are disclosed as inhibiting VEGF-RTKs. Such compounds are also disclosed in published. United States patent applications U.S. 2002/0107392 and U.S. 2003/0028018 and U.S. Pat. Nos. 6,605,617, 6,774,237, 6,762,194, and 6,800,760. Other such compounds are disclosed along with new uses of such compounds in inhibiting serine/threonine kinases and tyrosine kinases are disclosed in WO 2004/018419, and U.S. 2004/0092535, filed on Aug. 19, 2003, and claiming priority to each of the following provisional applications: U.S. Provisional Application No. 60/405,729 filed on Aug. 23, 2002; U.S. Provisional Application No.
  • the SU-5402 compound is 3-[3-(2-Carboxyethyl)-4-methylpyrrol-2-methylidenyl]-2-indolinone and has the following formula.
  • the PD-173074 compound has the compound structure and chemical name shown below.
  • the measurement of gene expression is performed on a sample, preferably a biological sample, obtained from the patient.
  • a sample preferably a biological sample
  • the patient may undergo a blood draw or tissue biopsy and the measurement may be made on the resulting sample.
  • the test may be performed on an isolated fraction of the sample or in situ.
  • Detection of the presence of gene expression of the biomarker of interest and/or detection of the level of alteration in the gene expression compared to baseline may be made utilizing standard techniques.
  • Detection can be by any appropriate method, including for example, detecting the quantity of mRNA transcribed from the gene or the quantity of cDNA produced from the reverse transcription of the mRNA transcribed from the gene or the quantity of the polypeptide or protein encoded by the gene. These methods can be performed on a sample by sample basis or modified for high throughput analysis. Additionally, databases containing quantitative full or partial transcripts or protein sequences isolated from a cell sample can be searched and analyzed for the presence and amount of transcript or expressed gene product.
  • nucleic acid contained in the aforementioned samples is first extracted according to standard methods in the art.
  • mRNA can be isolated using various lytic enzymes or chemical solutions according to the procedures set forth in Sambrook et al. (1989), supra or extracted by nucleic-acid-binding resins following the accompanying instructions provided by manufactures.
  • the mRNA of the biomarker contained in the extracted nucleic acid sample is then detected by hybridization (e.g. Northern blot analysis) and/or amplification procedures according to methods widely known in the art or based on the methods exemplified herein.
  • Nucleic acid molecules having at least 10 nucleotides and exhibiting sequence complementarity or homology to the biomarkers described herein find utility as hybridization probes. It is known in the art that a “perfectly matched” probe is not needed for a specific hybridization. Minor changes in probe sequence achieved by substitution, deletion or insertion of a small number of bases do not affect the hybridization specificity. In general, as much as 20% base-pair mismatch (when optimally aligned) can be tolerated.
  • probes or primers in combination with an appropriate means, such as a label, for detecting hybridization and therefore complementary sequences.
  • appropriate indicator means include fluorescent, radioactive, enzymatic or other ligands, such as avidin/biotin, which are capable of giving a detectable signal.
  • fluorescent label or an enzyme tag such as urease, alkaline phosphatase or peroxidase, instead of radioactive or other environmental undesirable reagents.
  • enzyme tags colorimetric indicator substrates are known which can be employed to provide a means visible to the human eye or spectrophotometrically, to identify specific hybridization with complementary nucleic acid-containing samples.
  • Hybridization reactions can be performed under conditions of different “stringency”. Relevant conditions include temperature, ionic strength, time of incubation, the presence of additional solutes in the reaction mixture such as formamide, and the washing procedure. Higher stringency conditions are those conditions, such as higher temperature and lower sodium ion concentration, which require higher minimum complementarity between hybridizing elements for a stable hybridization complex to form. Conditions that increase the stringency of a hybridization reaction are widely known and published in the art. See, for example, (Sambrook, et al., (1989), supra).
  • RNAs are isolated from cell or tissue samples as described above.
  • the gene transcripts can be converted to cDNA.
  • a sampling of the biomarker transcript(s) is/are subjected to sequence-specific analysis and quantified. These gene transcript sequence abundances are compared to the baseline.
  • any one of gene copy number, transcription, or translation of a biomarker can be determined using an amplification method such as PCR.
  • PCR General procedures for PCR are taught in MacPherson et al., PCR: A P RACTICAL A PPROACH , (IRL Press at Oxford University Press (1991)).
  • PCR conditions used for each application reaction are empirically determined. A number of parameters influence the success of a reaction. Among them are annealing temperature and time, extension time, Mg 2+ ATP concentration, pH, and the relative concentration of primers, templates, and deoxyribonucleotides.
  • the resulting DNA fragments can be detected by agarose gel electrophoresis followed by visualization with ethidium bromide staining and ultraviolet illumination.
  • the biomarkers are detected and quantitated by hybridization to a probe that specifically hybridizes to the appropriate probe for that biomarker.
  • the probes also can be attached to a solid support for use in high throughput screening assays using methods known in the art.
  • the probes of this invention are synthesized on a derivatized glass surface.
  • Photoprotected nucleoside phosphoramidites are coupled to the glass surface, selectively deprotected by photolysis through a photolithographic mask, and reacted with a second protected nucleoside phosphoramidite. The coupling/deprotection process is repeated until the desired probe is complete.
  • the expression level of the biomarker is determined through exposure of a nucleic acid sample to the probe-modified chip. Extracted nucleic acid is labeled, for example, with a fluorescent tag, preferably during an amplification step. Hybridization of the labeled sample is performed at an appropriate stringency level. The degree of probe-nucleic acid hybridization is quantitatively measured using a detection device, such as a confocal microscope. See U.S. Pat. Nos. 5,578,832 and 5,631,734.
  • the method is performed by the detecting and comparing of two or more biomarkers that have been pre-determined to be predictive of a therapeutic response.
  • a plurality of biomarkers e.g., see Tables I through V, supra, are used in the method of this invention.
  • the biomarkers or probes that specifically hybridize and recognize the biomarker of interest are arranged on a high density oligonucleotide probe array that provides an effective means of monitoring expression of a multiplicity of genes.
  • the methods of this invention are used to monitor expression of the genes which specifically hybridize to the probes of this invention in so response to defined stimuli, such as a drug or biologic.
  • the hybridized nucleic acids are detected by detecting one or more labels attached to the sample nucleic acids.
  • the labels may be incorporated by any of a number of means well known to those of skill in the art. However, in one aspect, the label is simultaneously incorporated during the amplification step in the preparation of the sample nucleic acid.
  • PCR polymerase chain reaction
  • labeled primers or labeled nucleotides will provide a labeled amplification product.
  • transcription amplification as described above, using a labeled nucleotide (e.g. fluorescein-labeled UTP and/or CTP) incorporates a label in to the transcribed nucleic acids.
  • a label may be added directly to the original nucleic acid sample (e.g., mRNA, polyA, mRNA, cDNA, etc.) or to the amplification product after the amplification is completed.
  • Means of attaching labels to nucleic acids are well known to those of skill in the art and include, for example nick translation or end-labeling (e.g. with a labeled RNA) by kinasing of the nucleic acid and subsequent attachment (ligation) of a nucleic acid linker joining the sample nucleic acid to a label (e.g., a fluorophore).
  • Detectable labels suitable for use in the present invention include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means.
  • Useful labels in the present invention include biotin for staining with labeled streptavidin conjugate, magnetic beads (e.g., DynabeadsTM), fluorescent dyes (e.g., fluorescein, texas red, rhodamine, green fluorescent protein, and the like), radiolabels (e.g., 3 H, 125 I, 35 S, 14 C, or 32 P) enzymes (e.g., horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (e.g., polystyrene, polypropylene, latex, etc.) beads.
  • Patents teaching the use of such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,
  • radiolabels may be detected using photographic film or scintillation counters
  • fluorescent markers may be detected using a photodetector to detect emitted light
  • Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label.
  • the label may be added to the target (sample) nucleic acid(s) prior to, or after the hybridization.
  • detectable labels that are directly attached to or incorporated into the target (sample) nucleic acid prior to hybridization.
  • indirect labels are joined to the hybrid duplex after hybridization.
  • the indirect label is attached to a binding moiety that has been attached to the target nucleic acid prior to the hybridization.
  • the target nucleic acid may be biotinylated before the hybridization. After hybridization, an avidin-conjugated fluorophore will bind the biotin bearing hybrid duplexes providing a label that is easily detected.
  • the nucleic acid sample also may be modified prior to hybridization to the high density probe array in order to reduce sample complexity thereby decreasing background signal and improving sensitivity of the measurement using the methods disclosed in WO 97/10365.
  • Results from the chip assay are typically analyzed using a computer software program. See, for example, EP 0717 113 A2 and WO 95/20681.
  • the hybridization data is read into the program, which calculates the expression level of the targeted gene(s).
  • the figures may be compared against existing data sets of gene expression levels for diseased and healthy individuals. A correlation between the obtained data and that of a set of a predetermined baseline identifies patients likely to be responsive to the therapy.
  • a data base useful for the identification of patients likely to respond to a predetermined therapy, e.g., anti-FGFR3 therapy
  • the database contains a combination of base line gene expression data against which the patient sample can be compared using bioinformatic techniques known in the art.
  • the pre-determined baseline information is stored in a digital storage medium such that a data processing system for standardized representation of the genes that identify patients that are responsive to therapy.
  • the data processing system is useful to analyze gene expression between two samples.
  • a suitable sample is isolated from the patient and then the genotype or phenotype of the cell or sample is determined using methods known in the art.
  • the nucleic acids of the biomarkers if present in the sample are sequenced and transcribed to code.
  • the sequences (in code form) from the sample are compared with the sequence(s) present in the database using homology search techniques.
  • Expression level of the biomarker can also be determined by examining the protein product. Determining the protein level involves (a) providing a biological sample containing expression product of the biomarker; and (b) measuring the amount of any immunospecific binding that occurs between an antibody that selectively recognizes and binds to the expression product of the biomarker in the sample, in which the amount of immunospecific binding indicates the level of the biomarker expression. This information is then compared to a pre-determined base line and analyzed to identify those patients suitable for therapy.
  • radioimmunoassays include but are not limited to radioimmunoassays, ELISA (enzyme linked immunoradiometric assays), “sandwich” immunoassays, immunoradiometric assays, in situ immunoassays (using e.g., colloidal gold, enzyme or radioisotope labels), western blot analysis, immunoprecipitation assays, immunoflourescent assays, and PAGE-SDS.
  • Antibodies that specifically recognize and bind to the protein products of the expression products of the biomarkers are required for immunoassays. These may be purchased from commercial vendors or generated and screened using methods well known in the art. See Harlow and Lane (1988) supra. and Sambrook et al. (1989) supra.
  • a patient may be beneficially treated by administration of an inhibitor of FGFR3, particularly a tyrosine kinase small molecule inhibitor (SMI) of FGFR3.
  • SMI small molecule inhibitor
  • treatment according to the invention may constitute administration of one or more small molecule FGFR3 inhibitors, such as those disclosed herein.
  • the small molecule inhibitors may be used in combination with other treatments.
  • inhibitors that are not small molecules e.g. biologicals, polynucleotides, gene therapy, etc. may be used for the ongoing treatment, in some cases, whereas the small molecule FGFR3 inhibitor may be used primarily as an initial aid in identifying candidates.
  • one inhibitor may be used prior to a gene expression level measurement step and another may be used subsequently.
  • the methods of the invention are useful for treatment of cellular proliferative disease and particularly neoplastic disease.
  • t(4; 14) translocation that is associated with the ectopic expression of the receptor tyrosine kinase fibroblast growth factor receptor 3 (FGFR3).
  • the t(4; 14) abnormality is typically diagnosed via a cytogenetic test, such as a fluorescence in situ hybridization (FISH) analysis, performed on a bone marrow aspirate taken from the patient.
  • FISH fluorescence in situ hybridization
  • the t(4; 14) multiple myeloma patient has a poor prognosis, but the methods taught herein offer new hope in that they may be employed to great advantage to identify such patients for treatment with an FGFR3 inhibitor, monitor response to treatment in such patients, as well as to aid in the development of new and/or optimized FGFR3 inhibitors.
  • Therapeutic agents utilized according to this invention include, but are not limited to small molecules. They may be polynucleotides, peptides, antibodies, antigen presenting cells and include immune effector cells that specifically recognize and lyse cells expressing the gene of interest. One can determine if a subject or patient will be beneficially treated by the use of agents by screening one or more of the agents against tumor cells isolated from the subject or patient using methods known in the art.
  • a therapeutic agent in accordance with the methods of the invention, e.g., encapsulation in liposomes, microparticles, microcapsules, expression by recombinant cells, receptor-mediated endocytosis (See e.g., Wu and Wu (1987) J. Biol. Chem. 262:4429-4432), construction of a therapeutic nucleic acid as part of a retroviral or other vector, etc.
  • Methods of delivery include but are not limited to intra-arterial, intra-muscular, intravenous, intranasal and oral routes.
  • Administration in vivo can be effected in one dose, continuously or intermittently throughout the course of treatment. Methods of determining the most effective means and dosage of administration are well known to those of skill in the art and will vary with the composition used for therapy, the purpose of the therapy, the target cell being treated and the subject being treated. Single or multiple administrations can be carried out with the dose level and pattern being selected by the treating physician. Suitable dosage formulations and methods of administering the agents may be empirically adjusted.
  • compositions utilized according to the methods of the invention can be administered orally, intranasally, parenterally or by inhalation therapy, and may take the form of tablets, lozenges, granules, capsules, pills, ampoules, suppositories or aerosol form. They may also take the form of suspensions, solutions and emulsions of the active ingredient in aqueous or nonaqueous diluents, syrups, granulates or powders. In addition to the key active ingredients, the pharmaceutical compositions can also contain other pharmaceutically active compounds or a plurality of compositions of the invention.
  • an agent administered according to the invention may be administered for therapy by any suitable route including oral, rectal, nasal, topical (including transdermal, aerosol, buccal and sublingual), vaginal, parental (including subcutaneous, intramuscular, intravenous and intradermal) and pulmonary. It will also be appreciated that the preferred route will vary with the condition and age of the recipient and the disease being treated.
  • the agent should be administered to achieve peak concentrations of the active compound at sites of disease. This may be achieved, for example, by the intravenous injection of the agent, optionally in saline or orally administered, for example, as a tablet, capsule or syrup containing the active ingredient. Desirable blood levels of the agent may be maintained by a continuous infusion to provide a therapeutic amount of the active ingredient within disease tissue.
  • operative combinations is contemplated to provide therapeutic combinations requiring a lower total dosage of each component antiviral agent than may be required when each individual therapeutic compound or drug is used alone, thereby reducing adverse effects.
  • the agent While it is possible for the agent to be administered alone, it is preferable to present it as a pharmaceutical formulation comprising at least one active ingredient, as defined above, together with one or more pharmaceutically acceptable carriers therefor and optionally other therapeutic agents.
  • Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient.
  • Formulations include those suitable for oral, rectal, nasal, topical (including transdermal, buccal and sublingual), vaginal, parenteral (including subcutaneous, intramuscular, intravenous and intradermal) and pulmonary administration.
  • the formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. Such methods include the step of bringing into association the active ingredient with the carrier which constitutes one or more accessory ingredients. In general, the formulations are prepared by uniformly and intimately bringing into association the active ingredient with liquid carriers or finely divided solid carriers or both and then, if necessary, shaping the product.
  • Formulations suitable for oral administration may be presented as discrete units such as capsules, cachets or tablets, each containing a predetermined amount of the active ingredient; as a powder or granules; as a solution or suspension in an aqueous or non-aqueous liquid; or as an oil-in-water liquid emulsion or a water-in-oil liquid emulsion.
  • the active ingredient may also be presented a bolus, electuary or paste.
  • a tablet may be made by compression or molding, optionally with one or more accessory ingredients.
  • Compressed tablets may be prepared by compressing in a suitable machine the active ingredient in a free-flowing form such as a powder or granules, optionally mixed with a binder (e.g., povidone, gelatin, hydroxypropylmethyl cellulose), lubricant, inert diluent, preservative, disintegrant (e.g., sodium starch glycolate, cross-linked povidone, cross-linked sodium carboxymethyl cellulose) surface-active or dispersing agent.
  • Molded tablets may be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent.
  • the tablets may optionally be coated or scored and may be formulated so as to provide slow or controlled release of the active ingredient therein using, for example, hydroxypropylmethyl cellulose in varying proportions to provide the desired release profile. Tablets may optionally be provided with an enteric coating, to provide release in parts of the gut other than the stomach.
  • Formulations suitable for topical administration in the mouth include lozenges comprising the active ingredient in a flavored basis, usually sucrose and acacia or tragacanth; pastilles comprising the active ingredient in an inert basis such as gelatin and glycerin or sucrose and acacia; and mouthwashes comprising the active ingredient in a suitable liquid carrier.
  • compositions for topical administration may be formulated as an ointment, cream, suspension, lotion, powder, solution, past, gel, spray, aerosol or oil.
  • a formulation may comprise a patch or a dressing such as a bandage or adhesive plaster impregnated with active ingredients and optionally one or more excipients or diluents.
  • the aqueous phase of the cream base may include, for example, at least about 30% w/w of a polyhydric alcohol, i.e., an alcohol having two or more hydroxyl groups such as propylene glycol, butane-1,3-diol, mannitol, sorbitol, glycerol and polyethylene glycol and mixtures thereof.
  • the topical formulations may desirably include a compound which enhances absorption or penetration of the agent through the skin or other affected areas. Examples of such dermal penetration enhancers include dimethylsulfoxide and related analogues.
  • the oily phase of the emulsions of a composition used according to this invention may be constituted from known ingredients in a known manner. While this phase may comprise merely an emulsifier (otherwise known as an emulgent), it desirably comprises a mixture of at least one emulsifier with a fat or an oil or with both a fat and an oil. Preferably, a hydrophilic emulsifier is included together with a lipophilic emulsifier which acts as a stabilizer. It is also preferred to include both an oil and a fat.
  • the emulsifier(s) with or without stabilizer(s) make up the so-called emulsifying wax
  • the wax together with the oil and/or fat make up the so-called emulsifying ointment base which forms the oily dispersed phase of the cream formulations.
  • Emulgents and emulsion stabilizers suitable for use in the formulation of the present invention include Tween 60, Span 80, cetostearyl alcohol, myristyl alcohol, glyceryl monostearate and sodium lauryl sulphate.
  • the choice of suitable oils or fats for the formulation is based on achieving the desired cosmetic properties, since the solubility of the active compound in most oils likely to be used in pharmaceutical emulsion formulations is very low.
  • the cream should preferably be a non-greasy, non-staining and washable product with suitable consistency to avoid leakage from tubes or other containers.
  • Straight or branched chain, mono- or dibasic alkyl esters such as di-isoadipate, isocetyl stearate, propylene glycol diester of coconut fatty acids, isopropyl myristate, decyl oleate, isopropyl palmitate, butyl stearate, 2-ethylhexyl palmitate or a blend of branched chain esters known as Crodamol CAP may be used, the last three being preferred esters. These may be used alone or in combination depending on the properties required.
  • mono-isoadipate such as di-isoadipate, isocetyl stearate, propylene glycol diester of coconut fatty acids, isopropyl myristate, decyl oleate, isopropyl palmitate, butyl stearate, 2-ethylhexyl palmitate or a blend of branched chain esters known as Crodamol CAP may be used, the
  • high melting point lipids such as white soft paraffin and/or liquid paraffin or other mineral oils can be used.
  • Formulations suitable for topical administration to the eye also include eye drops wherein the active ingredient is dissolved or suspended in a suitable carrier, especially an aqueous solvent for the agent.
  • Formulations for rectal administration may be presented as a suppository with a suitable base comprising, for example, cocoa butter or a salicylate.
  • Formulations suitable for vaginal administration may be presented as pessaries, tampons, creams, gels, pastes, foams or spray formulations containing in addition to the agent, such carriers as are known in the art to be appropriate.
  • Formulations suitable for nasal administration wherein the carrier is a solid, include a coarse powder having a particle size, for example, in the range of about 20 to about 500 microns which is administered in the manner in which snuff is taken, i.e., by rapid inhalation through the nasal passage from a container of the powder held close up to the nose.
  • Suitable formulations wherein the carrier is a liquid for administration as, for example, nasal spray, nasal drops or by aerosol administration by nebulizer include aqueous or oily solutions of the agent.
  • Formulations suitable for parenteral administration include aqueous and non-aqueous isotonic sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents, thickening agents and liposomes or other microparticulate systems which are designed to target the compound to blood components or one or more organs.
  • the formulations may be presented in unit-dose or multi-dose sealed containers, for example, ampoules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example water for injections, immediately prior to use.
  • Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets of the kind previously described.
  • Preferred unit dosage formulations are those containing a daily dose or unit, daily subdose, as herein above-recited, or an appropriate fraction thereof, of an agent.
  • Transcriptional activity was assessed by measuring levels of messenger RNA (mRNA) in cells derived from human multiple myeloma tumors using Affymetrix HG-U133-Plus-2 GeneChips.
  • mRNA messenger RNA
  • mRNA in cells treated with the small molecule inhibitors SU-5402, PD-173074 (both Pfizer Inc.) and CHIR-258 (Chiron Corp.), with FGF ligand, or with FGFR3 silencing RNA (siRNA) was quantitatively compared to expression in untreated cells (or cells treated with a scrambled siRNA control in the latter case). Specific differences and similarities to the other FGFR3 inhibitors were compared with CHIR-258.

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Abstract

Methods of utilizing biomarkers to identify patients for treatment or to monitor response to treatment are taught herein. Alterations in levels of gene expression of the biomarkers, particularly in response to FGFR3 inhibition, are measured and identifications or adjustments may be made accordingly.

Description

    BACKGROUND OF THE INVENTION
  • The present invention relates generally to the field of pharmacogenomics and in particular to the use of biomarkers for identifying patients suitable for treatment as well as to methods of following their response to methods of treatment.
  • An effort to understand an individual patient's response or disease progression is the topic of present day research. Indeed, the field of pharmacogenomics or pharmacogenetics utilizes genomic data, pharmacology, and medicine, and often relies on advanced research tools to correlate genetic variability to one or more of predisposition to a disease and/or its progression, as well as therapeutic response to a drug or therapeutic regimen. Typically, multiple genes are analyzed simultaneously in a large-scale, genome-wide approach.
  • Proliferative cell disorders such as cancers usually develop through the accumulation of a series of mutations in the patient's DNA within a subpopulation of cells. These mutations may confer a survival advantage on the cells that causes them to grow and spread in an uncontrolled manner that is deleterious to the surrounding tissues. The particular set of mutations may be unique to an individual patient's tumor. Cancers of the same tissue or organ in different individuals may have originated from different sets of mutations, though certain mutations may be prevalent among particular cancer types. The characteristic set of mutations will determine how the cancer cells behave, and in particular, their likelihood of response to a given therapeutic regimen.
  • One may characterize the genetic alterations in a tumor by using advanced research tools that measure the genetic sequence of the tumor's DNA, or the RNA or proteins that are the expression of the altered DNA. It is a goal of current research to identify characteristics of an individual's tumor that are predictive of the likelihood of that tumor's response to various therapeutic treatments. Thus, one or more genes would be identified where presence of particular genetic mutations in the DNA, or their levels of expression, either as RNA transcripts or as proteins, or a combination of these factors, would be predictive of the likelihood that a particular treatment would affect the tumor in a manner that would be beneficial to the patient.
  • One main purpose is to determine which variations in individuals or subpopulations, associated with their genetics or the genetic characteristics of their disease, factor into drug efficacy and to create suitable tests, including diagnostic tests. Drugs that are tailored for patients with a particular genetic sequence, or for diseases characterized by particular genetic alterations, may thus be produced. The tests may also be used to guide treatment decisions, such as which drug or drug combination is mostly likely to be beneficial to the patient, and what dosing and schedule is most appropriate. Diagnostic tests and genetic profiling will help avoid the expense and the potentially detrimental trial-and-error approach to the suitability of a particular treatment regimen or a particular dosage level.
  • While the era of customized drugs may be coming, methods that utilize genetic information to identify specific individuals or subgroups for a particular type of treatment or optimization of a treatment may be immediately put to use today.
  • An individual's response to a particular treatment or predisposition to disease and the correlation to a particular gene of interest has been documented. It is now believed that cancer chemotherapy is limited by the predisposition of specific populations to drug toxicity or poor drug response. For a review of the use of germline polymorphisms in clinical oncology, see Lenz, H.-J. (2004) J. Clin. Oncol. 22(13):2519-2521. For a review of pharmacogenctic and pharmacogenomics in therapeutic antibody development for the treatment of cancer, see Yan and Beckman (2005) Biotechniques 39:565-568.
  • Results from numerous studies suggest several genes may play a major role in the principal pathways of cancer progression and recurrence, and that the corresponding germ-line polymorphisms may lead to significant differences at transcriptional and/or translational levels. Polymorphism has been linked to cancer susceptibility (oncogenes, tumor suppressor genes, and genes of enzymes involved in metabolic pathways) of individuals. In patients younger than 35 years, several markers for increased cancer risk have been identified. Cytochrome P4501A1 and gluthathione S-transferase M1 genotypes influence the risk of developing prostate cancer in younger patients. Similarly, mutations in the tumor suppressor gene, p53, are associated with brain tumors in young adults.
  • This approach may be extended to mutations that are specific to cancer cells, and not otherwise found in the patient's genome. For instance, it has been demonstrated clinically in patients with gastrointestinal stromal tumors (GIST) treated with the drug Gleevec (imatinib mesylate; Novartis) that particular activating mutations in the genes KIT and PDGFA are linked to higher response rates to the drug, see J Clin Oncol. 2003 Dec. 1; 21(23):4342-9.
  • By measuring changes in gene expression of cancer cell lines induced by treatment with a particular therapeutic agent, one may characterize the cells' response to that agent. This approach provides insight into the mechanism of the drug, including what biological processes or pathways it impacts. Such information can help guide the treatment of patients, by providing expectations as to which genes will change in response to treatment. An assay of those genes from a sample collected from a patient post-treatment could then be used to determine whether the drug was having the intended effect, and by extension, whether the dose or schedule should be altered, or the regimen discontinued. This approach would improve efficacy by ensuring that patients receive the most appropriate treatment.
    • SUMMARY OF THE INVENTION
  • One embodiment of the invention relates to a method of identifying a patient for treatment. The method may optionally include an administration of an FGFR3 inhibitor to the patient prior to measurement of gene expression on a sample obtained from the patient. The gene expression analysis is intended to detect the presence and/or alteration in level of expression of biomarkers disclosed herein. Notable detection or alteration in the levels compared to baseline levels is indicative of the candidacy of the patient for treatment.
  • Another embodiment of the invention comprises a method of monitoring response of a patient to treatment. The method may include the step of administration of an FGFR3 inhibitor to the patient prior to measurement of gene expression on a sample obtained from the patient. Alternatively, monitoring may be conducted on a sample obtained from a patient who has previously been treated so that an administration step by one practicing the method of monitoring response is not required. Detection of an alteration in the level of expression of at least one biomarker compared to baseline is indicative of a favorable response of the patient to the treatment.
  • Another aspect of the invention is a method of utilizing a biomarker in treatment of a patient. An FGFR3 inhibitor may be administered and gene expression level of one or more biomarkers tested. Thereafter, the same or a different inhibitor may be administered in the treatment.
  • Yet another aspect of the invention is a method of treatment for multiple myeloma. The method utilizes an agent that alters the level of expression of one or more of the identified biomarkers.
  • A method of adjusting a dosage amount of an inhibitor of FGFR3 for treatment of a cell proliferative disorder in a patient is also taught herein. The method comprises administering an initial amount of the inhibitor of FGFR3 to the patient, monitoring gene expression on a sample from the patient for at least one of the identified biomarkers and adjusting the dosage amount for subsequent administration to the patient, depending on the level of expression of the biomarker or biomarkers that has occurred upon administration of the initial amount.
  • A further embodiment of the invention is a method of utilizing a biomarker to identify an FGFR3 inhibitory compound for potential treatment or further development.
    • DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
  • The invention is an example of translational medicine at work, wherein patients may be treated selectively based on their particular genetic profile.
    • DEFINITIONS AND TECHNIQUES
  • The practice of the present invention will employ, unless otherwise indicated, conventional techniques of immunology, molecular biology, microbiology, cell biology and recombinant DNA, which are within the skill of the art. See e.g., Sambrook, Fritsch and Maniatis, MOLECULAR CLONING: A LABORATORY MANUAL, 2nd edition (1989); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel et al. eds., (1987)); the series METHODS IN ENZYMOLOGY (Academic Press, Inc.): PCR 2: A PRACTICAL APPROACH (M. J. MacPherson, B. D. Hames and G. R. Taylor eds. (1995)), Harlow and Lane, eds. (1988) ANTIBODIES, A LABORATORY MANUAL and ANIMAL CELL CULTURE (R. I. Freshney, ed. (1987)).
  • As used herein, certain, terms have the following defined meanings.
  • As used in the specification and claims, the singular form “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a cell” includes a plurality of cells, including mixtures thereof.
  • All numerical designations, e.g., pH, temperature, time, concentration, and molecular weight, including ranges, are approximations which are varied (+) or (−) by increments of 0.1. It is to be understood, although not always explicitly stated that all numerical designations are preceded by the term “about”. It also is to be understood, although not always explicitly stated, that the reagents described herein are merely exemplary and that equivalents of such are known in the art.
  • The terms “polynucleotide” and “oligonucleotide” are used interchangeably and refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides or analogs thereof. Polynucleotides can have any three-dimensional structure and may perform any function, known or unknown. The following are non-limiting examples of polynucleotides: a gene or gene fragment (for example, a probe, primer, EST or SAGE tag), exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A polynucleotide can comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure can be imparted before or after assembly of the polymer. The sequence of nucleotides can be interrupted by non-nucleotide components. A polynucleotide can be further modified after polymerization, such as by conjugation with a labeling component. The term also refers to both double- and single-stranded molecules. Unless otherwise specified or required, any embodiment of this invention that is a polynucleotide encompasses both the double-stranded form and each of two complementary single-stranded forms known or predicted to make up the double-stranded form.
  • A polynucleotide is composed of a specific sequence of four nucleotide bases: adenine (A); cytosine (C); guanine (G); thymine (T); and uracil (U) for guanine when the polynucleotide is RNA. Thus, the term “polynucleotide sequence” is the alphabetical representation of a polynucleotide molecule. This alphabetical representation can be input into databases in a computer having a central processing unit and used for bioinformatics applications such as functional genomics and homology searching.
  • A “gene” refers to a polynucleotide containing at least one open reading frame (ORE) that is capable of encoding a particular polypeptide or protein after being transcribed and translated. A polynucleotide sequence may be used to identify larger fragments or full-length coding sequences of the gene with which they are associated. Methods of isolating larger fragment sequences are known to those of skill in the art.
  • A “gene product” or alternatively a “gene expression product” refers to the amino acid (e.g., peptide or polypeptide) generated when a gene is transcribed and translated.
  • The term “polypeptide” is used interchangeably with the term “protein” and in its broadest sense refers to a compound of two or more subunit amino acids, amino acid analogs, or peptidomimetics. The subunits may be linked by peptide bonds. In another embodiment, the subunit may be linked by other bonds, e.g., ester, ether, etc.
  • As used herein the term “amino acid” refers to either natural and/or unnatural or synthetic amino acids, and both the D and L optical isomers, amino acid analogs, and peptidomimetics.
  • A peptide of three or more amino acids is commonly called an oligopeptide if the peptide chain is short. If the peptide chain is long, the peptide is commonly called a polypeptide or a protein.
  • As used herein, the term “comprising” is intended to mean that the methods include the recited elements, but do not exclude others. “Consisting essentially of” when used to define compositions and methods, shall mean excluding other elements of any essential significance to the combination. Thus, for example, a composition consisting essentially of elements as listed would not exclude trace contaminants from the isolation and purification method and pharmaceutically acceptable carriers, such as phosphate buffered saline, preservatives and the like. “Consisting of” shall mean excluding more than trace elements of other ingredients and substantial method steps of this invention. Embodiments defined by each of these transition terms are within the scope of this invention.
  • The term “isolated” means separated from constituents, cellular and otherwise, in which the polynucleotide, peptide, polypeptide, protein, antibody or fragments) thereof, are normally associated within nature. In one aspect of this invention, an isolated polynucleotide is separated from the 3′ and 5′ contiguous nucleotides with which it is normally associated within its native or natural environment, e.g., on the chromosome. As is apparent to those of skill in the art, a non-naturally occurring polynucleotide, peptide, polypeptide, protein, antibody, or fragment(s) thereof, does not require “isolation” to distinguish it from its naturally occurring counterpart. In addition, a “concentrated”, “separated” or “diluted” polynucleotide, peptide, polypeptide, protein, antibody or fragment(s) thereof, is distinguishable from its naturally occurring counterpart in that the concentration or number of molecules per volume is greater in a “concentrated” version or less than in a “separated” version than that of its naturally occurring counterpart. A polynucleotide, peptide, polypeptide, protein, antibody, or fragment(s) thereof, which differs from the naturally occurring counterpart in its primary sequence or, for example, by its glycosylation pattern, need not be present in its isolated form since it is distinguishable from its naturally occurring so counterpart by its primary sequence or, alternatively, by another characteristic such as glycosylation pattern. Thus, a non-naturally occurring polynucleotide is provided as a separate embodiment from the isolated naturally occurring polynucleotide. A protein produced in a bacterial cell is provided as a separate embodiment from the naturally occurring protein isolated from a eukaryotic cell in which it is produced in nature.
  • A “probe” when used in the context of polynucleotide manipulation refers to an oligonucleotide that is provided as a reagent to detect a target potentially present in a sample of interest by hybridizing with the target. Usually, a probe will comprise a label or a means by which a label can be attached, either before or subsequent to the hybridization reaction. Suitable labels include, but are not limited to radioisotopes, fluorochromes, chemiluminescent compounds, dyes, and proteins, including enzymes.
  • A “primer” is a short polynucleotide, generally with a free 3′-OH group that binds to a target or “template” potentially present in a sample of interest by hybridizing with the target, and thereafter promoting polymerization of a polynucleotide complementary to the target. A “polymerase chain reaction” (“PCR”) is a reaction in which replicate copies are made of a target polynucleotide using a “pair of primers” or a “set of primers” consisting of an “upstream” and a “downstream” primer, and a catalyst of polymerization, such as a DNA polymerase, and typically a thermally-stable polymerase enzyme. Methods for PCR are well known in the art, and taught, for example in “PCR: A PRACTICAL APPROACH” (M. MacPherson et al., IRL Press at Oxford University Press (1991)). All processes of producing replicate copies of a polynucleotide, such as PCR or gene cloning, are collectively referred to herein as “replication.” A primer can also be used as a probe in hybridization reactions, such as Southern or Northern blot analyses. Sambrook et al., supra.
  • As used herein, “expression” refers to the process by which polynucleotides are transcribed into mRNA and/or the process by which the transcribed mRNA is subsequently translated into peptides, polypeptides or proteins. If the polynucleotide is derived from genomic DNA, expression may include splicing of the mRNA in a eukaryotic cell. “Differentially expressed” as applied to a gene, refers to the differential production of the mRNA transcribed and/or translated from the gene or the protein product encoded by the gene. A differentially expressed gene may be overexpressed or underexpressed as compared to the expression level of a normal or control cell. However, as used herein overpression generally is at least 1.25 fold or, alternatively, at least 1.5 fold or, alternatively, at least 2 fold expression, or alternatively, at least 4 fold expression over that detected in a normal or healthy counterpart cell or tissue. The term “differentially expressed” also refers to nucleotide sequences in a cell or tissue which are expressed where silent in a control cell or not expressed where expressed in a control cell.
  • A high expression level of the gene may occur because of over expression of the gene or an increase in gene copy number. The gene may also be translated into more protein because of deregulation of a negative regulator.
  • A “gene expression profile” refers to a pattern of expression of a set of genes that recurs in multiple samples and reflects a property shared by those samples, such as tissue type, response to a particular treatment, or activation of a particular biological process or pathway in the cells. Furthermore, a gene expression profile differentiates between samples that share that common property and those that do not with better accuracy than would likely be achieved by assigning the samples to the two groups at random. A gene expression profile may be used to predict whether samples of unknown status share that common property or not. Some variation between the levels of the individual genes of the set and the typical profile is to be expected, but the overall similarity of the expression levels to the typical profile is such that it is statistically unlikely that the similarity would be observed by chance in samples not sharing the common property that the expression profile reflects.
  • An expression “database” denotes a set of stored data that represent a collection of sequences, which in turn represent a collection of biological reference materials.
  • The term “cDNAs” refers to complementary DNA, i.e. mRNA molecules present in a cell or organism made into cDNA with an enzyme such as reverse transcriptase. A “cDNA library” is a collection of all of the mRNA molecules present in a cell or organism, all turned into cDNA molecules with the enzyme reverse transcriptase, then inserted into “vectors” (other DNA molecules that can continue to replicate after addition of foreign DNA). Exemplary vectors for libraries include bacteriophage (also known as “phage”), viruses that infect bacteria, for example, lambda phage. The library can then be probed for the specific cDNA (and thus mRNA) of interest.
  • As used herein, “solid phase support” or “solid support”, used interchangeably, is not limited to a specific type of support. Rather a large number of supports are available and are known to one of ordinary skill in the art. Solid phase supports include silica gels, resins, derivatized plastic films, glass beads, cotton, plastic beads, alumina gels, microarrays, and chips. As used herein, “solid support” also includes synthetic antigen-presenting matrices, cells, and liposomes. A suitable solid phase support may be selected on the basis of desired end use and suitability for various protocols. For example, for peptide synthesis, solid phase support may refer to resins such as polystyrene (e.g., PAM-resin obtained from Bachem Inc., Peninsula Laboratories, etc.), POLYHIPE® resin (obtained from Aminotech, Canada), polyamide resin (obtained from Peninsula Laboratories), polystyrene resin grafted with polyethylene glycol (TentaGel®, Rapp Polymere, Tubingen, Germany), or polydimethylacrylamide resin (obtained from Milligen/Biosearch, Calif.).
  • A polynucleotide also can be attached to a solid support for use in high throughput screening assays. PCT WO 97/10365, for example, discloses the construction of high density oligonucleotide chips. See also, U.S. Pat. Nos. 5,405,783; 5,412,087; and 5,445,934. Using this method, the probes are synthesized on a derivatized glass surface to form chip arrays. Photoprotected nucleoside phosphoramidites are coupled to the glass surface, selectively deprotected by photolysis through a photolithographic mask and reacted with a second protected nucleoside phosphoramidite. The coupling/deprotection process is repeated until the desired probe is complete.
  • As an example, transcriptional activity may be assessed by measuring levels of messenger RNA using a gene chip such as the Affymetrix HG-U133-Plus-2 GeneChips. High-throughput, real-time quanititation of RNA (of hundreds of genes simultaneously) thus becomes possible in a reproducible system.
  • “Hybridization” refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues. The hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding or in any other sequence-specific mariner. The complex may comprise two strands forming a duplex structure, three or more strands forming a multi-stranded complex, a single self-hybridizing strand, or any combination of these. A hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PCR reaction or the enzymatic cleavage of a polynucleotide by a ribozyme.
  • Hybridization reactions can be performed under conditions of different “stringency”. In general, a low stringency hybridization reaction is carried out at about 40° C. in 10×SSC or a solution of equivalent ionic strength/temperature. A moderate stringency hybridization is typically performed at about 50° C. in 6×SSC, and a high stringency hybridization reaction is generally performed at about 60° C. in 1×SSC.
  • When hybridization occurs in an antiparallel configuration between two single-stranded polynucleotides, the reaction is called “annealing” and those polynucleotides are described as “complementary”. A double-stranded polynucleotide can be “complementary” or “homologous” to another polynucleotide, if hybridization can occur between one of the strands of the first polynucleotide and the second. “Complementarity” or “homology” (the degree that one polynucleotide is complementary with another) is quantifiable in terms of the proportion of bases in opposing strands that are expected to form hydrogen bonding with each other, according to generally accepted base-pairing rules.
  • A polynucleotide or polynucleotide region (or a polypeptide or polypeptide region) has a certain percentage (for example, 80%, 85%, 90%, or 95%) of “sequence identity” to another sequence means that, when aligned, that percentage of bases (or amino acids) are the same in comparing the two sequences. This alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel et al., eds., 1987) Supplement 30, section 7.7.18, Table 7.7.1. Preferably, default parameters are used for alignment. A preferred alignment program is BLAST, using default parameters. In particular, preferred programs are BLASTN and BLASTP, using the following default parameters: Genetic code=standard; filter=none; strand=both; cutoff=60; expect=10; Matrix=BLOSUM62; Descriptions=50 sequences; sort by=HIGH SCORE; Databases=non-redundant, GenBank EMBL+DDBJ+PDB GenBank CDS translations+SwissProtein+SPupdate+PIR. Details of these programs can be found at the following Internet address: www.ncbi.nih.gov/cgi-bin/BLAST.
  • The term “cell proliferative disorders” shall include dysregulation of normal physiological function characterized by abnormal cell growth and/or division or loss of function. Examples of “cell proliferative disorders” includes but is not limited to hyperplasia, neoplasia, metaplasia, and various autoimmune disorders, e.g., those characterized by the dysregulation of T cell apoptosis.
  • Hyperplasia is a form of controlled cell proliferation involving an increase in cell number in a tissue or organ, without significant alteration in structure or function. Metaplasia is a form of controlled cell growth in which one type of fully differentiated cell substitutes for another type of differentiated cell. Metaplasia can occur in epithelial or connective tissue cells. Atypical metaplasia involves a somewhat disorderly metaplastic epithelium.
  • As used herein, the terms “neoplastic cells,” “neoplastic disease,” “neoplasia,” “tumor,” “tumor cells,” “cancer,” and “cancer cells,” (used interchangeably) refer to cells which exhibit relatively autonomous growth, so that they exhibit an aberrant growth phenotype characterized by a significant loss of control of cell proliferation (i.e., de-regulated cell division). Neoplastic cells can be malignant or benign. A metastatic cell or tissue means that the cell can invade and destroy neighboring body structures.
  • “Suppressing” tumor growth indicates a growth state that is curtailed when compared to growth without contact with educated, antigen-specific immune effector cells. Tumor cell growth can be assessed by any means known in the art, including, but not limited to, measuring tumor size, determining whether tumor cells are proliferating using a 3H-thymidine incorporation assay or counting tumor cells. “Suppressing” tumor cell growth means any or all of the following states: slowing, delaying and stopping tumor growth, as well as tumor shrinkage.
  • A “composition” is also intended to encompass a combination of active agent and another carrier, e.g., compound or composition, inert (for example, a detectable agent or label) or active, such as an adjuvant, diluent, binder, stabilizer, buffers, salts, lipophilic solvents, preservative, adjuvant or the like. Carriers also include pharmaceutical excipients and additives proteins, peptides, amino acids, lipids, and carbohydrates (e.g., sugars, including monosaccharides, di-, tri-, tetra-, and oligosaccharides; derivatized sugars such as alditols, aldonic acids, esterified sugars and the like; and polysaccharides or sugar polymers), which can be present singly or in combination, comprising alone or in combination 1-99.99% by weight or volume. Exemplary protein excipients include serum albumin such as human serum albumin (HSA), recombinant human albumin (rHA), gelatin, casein, and the like. Representative amino acid/antibody components, which can also function in a buffering capacity, include alanine, glycine, arginine, betaine, histidine, glutamic acid, aspartic acid, cysteine, lysine, leucine, isoleucine, valine, methionine, phenylalanine, aspartame, and the like. Carbohydrate excipients are also intended within the scope of this invention, examples of which include but are not limited to monosaccharides such as fructose, maltose, galactose, glucose, D-mannose, sorbose, and the like; disaccharides, such as lactose, sucrose, trehalose, cellobiose, and the like; polysaccharides, such as raffinose, melezitose, maltodextrins, dextrans, starches, and the like; and alditols, such as mannitol, xylitol, maltitol, lactitol, xylitol sorbitol (glucitol) and myoinositol.
  • The term carrier further includes a buffer or a pH adjusting agent; typically, the buffer is a salt prepared from an organic acid or base. Representative buffers include organic acid salts such as salts of citric acid, ascorbic acid, gluconic acid, carbonic acid, tartaric acid, succinic acid, acetic acid, or phthalic acid; Tris, tromethamine hydrochloride, or phosphate buffers. Additional carriers include polymeric excipients/additives such as polyvinylpyrrolidones, ficolls (a polymeric sugar), dextrates (e.g., cyclodextrins, such as 2-hydroxypropyl-.quadrature.-cyclodextrin), polyethylene glycols, flavoring agents, antimicrobial agents, sweeteners, antioxidants, antistatic agents, surfactants (e.g., polysorbates such as “TWEEN 20” and “TWEEN 80”), lipids (e.g., phospholipids, fatty acids), steroids (e.g., cholesterol), and chelating agents (e.g., EDTA).
  • As used herein, the term “pharmaceutically acceptable carrier” encompasses any of the standard pharmaceutical carriers, such as a phosphate buffered saline solution, water, and emulsions, such as an oil/water or water/oil emulsion, and various types of wetting agents.
  • The compositions also can include stabilizers and preservatives and any of the above noted carriers with the additional provisio that they be acceptable for use in vivo. For examples of carriers, stabilizers and adjuvants, see Martin REMINGTON'S PHARM. SCI., 15th Ed. (Mack Publ. Co., Easton (1975) and Williams & Williams, (1995), and in the “PHYSICIAN'S DESK REFERENCE”, 52nd ed., Medical Economics, Montvale, N.J. (1998).
  • An “effective amount” is an amount sufficient to effect beneficial or desired results. An effective amount can be administered in one or more administrations, applications or dosages.
  • A “subject,” “individual” or “patient” is used interchangeably herein, which refers to a vertebrate, preferably a mammal, more preferably a human. Mammals include, but are not limited to, murines, simians, humans, farm animals, sport animals, and pets.
  • “FGFR3” is the acronym for fibroblast growth factor receptor 3. The fibroblast growth factors are a family of polypeptide growth factors involved in a variety of activities, including mitogenesis, angiogenesis, and wound healing. They contain an extracellular domain with either 2 or 3 immunoglobulin (Ig)-like domains, a transmembrane domain, and a cytoplasmic tyrosine kinase domain. FGFR3 was cloned by Keegan et al., PNAS, 88:1095-1099 (1991). Inhibition of activated FGFR3 in t(4; 14) multiple myeloma patients is thought to lead to apoptosis. Trudel, et al., Blood, 105(7):2941-2948 (2005); Grand, et al., Leukemia, 18:962-966 (2004).
  • An “inhibitor” of FGFR3 as used herein binds or blocks or diminishes the effect of the FGFR3. Examples include, but are not limited to CHIR-258 and related compounds, SU-5402, PD-173074, and siRNA.
  • A “biomarker” is a distinctive indicator or specific feature or characteristic of a biological process or event. As used herein, a biomarker is a gene. A biomarker may be especially useful for measuring the progress of a disease or the response to a given treatment. In addition to assessing prognosis, in some instances, it may be used to diagnose an illness or screen for patients within a category, such as those most likely to respond to a certain type of treatment. A biomarker may also be useful in guiding the development or administration of an agent for treatment of a disease.
  • As noted above, the invention provides methods of identifying patients suitable for treatment and methods of monitoring response in patients receiving treatment. Also provided are methods of treatment and methods of adjusting dosage amounts by utilizing the biomarkers disclosed herein. Methods of identifying the appropriate inhibitory compound are also within the scope of the invention.
  • The present invention also provides a screen for various agents and methods that may supplement or replace the anti-FGFR3 therapy known in the art. In one aspect, the agent, alone or in combination with another agent or therapy method, is provided to the patient. After administration, a sample from the patient is screened for expression of one or more biomarkers identified herein and then compared to a pre-determined baseline.
  • Kits containing an FGFR3 inhibitor and instructions necessary to perform a method of the invention also are within the scope of the invention.
  • Further details regarding the practice of the invention are discussed below.
    • Biomarkers
  • Panels of genes have now been identified, whose expression correlates with the inhibition of FGFR3. The presence or absence of gene expression or the level or amount of gene expression of one or more of the biomarkers identified herein may be used to guide treatment decisions and measure responsiveness of the patient to a given type of treatment. For example, detection of the presence or lack thereof of gene expression or alteration of the level of gene expression compared to a predetermined baseline of one or more of the biomarkers identified in Tables I-V provides information regarding whether a patient may be a suitable candidate for treatment by CHIR-258 or another FGFR3 inhibitor.
  • It should be noted that any or all of the following biomarkers may be of particular interest: CCL3, LOC150271, CD48, DUSP4, ITGB7, DUSP6, ANXA9, CR2, AL531683, ZNF589, AW274468, FRMD3, LTB, and WDR42A.
  • As is apparent to one of skill in the art, gene expression can be measured by detecting the presence or absence, or presence and/or absolute or relative quantity of a gene expression product (e.g., RNA, mRNA, or the protein or polypeptide transcript) or the alteration in gene copy number. In some embodiments, altered expression is likely the result of an increase in copy number. In alternative embodiment, altered expression is likely the result of the loss of function of another gene such as a tumor suppressor or other negative regulator. In yet a further embodiment, expression is altered by the “turning on” of an enhancer. Accordingly, the specific method used to detect altered expression, as compared to the control or baseline, may be different and dependent on the particular biomarker selected. In yet further embodiments, the method requires analysis of gene expression of one or more predetermined biomarkers by more than one method, e.g., by use of immunohistochemical and molecular techniques such as a gene chip or array.
    • Tables
  • Tables I through V are presented below and constitute an integral part of this disclosure.
  • Table I is a list of biomarkers whose expression is indicative of activity related to FGFR3 inhibition.
  • Table II is a preferred subset of Table I according to one aspect of the invention, listing biomarkers generally having a higher level of alteration of gene expression compared to baseline in response to FGFR3 inhibition.
  • Table III is more preferred subset of Table I according to one aspect of the invention, listing biomarkers generally having the highest level of alteration of gene expression compared to so baseline in response to FGFR3 inhibition.
  • Table IV is a preferred subset of Table I according to a second aspect of the invention, listing biomarkers generally exhibiting the strongest correlation of gene expression in response to FGFR3 inhibition by the preferred compound, CHIR-258.
  • Table V is a more preferred subset of Table I according to a second aspect of the invention, listing biomarkers generally exhibiting the strongest correlation of gene expression in response to FGFR3 inhibition by the preferred compound, CHTR-258, in preference to either SU-5402 or PD-173074.
  • In each of Tables I through V, the biomarkers are shown with Entrez Gene ID Number (referring to the National Cancer Institute database identifier), Gene Symbol, and Gene Description.
  • TABLE I
    ENTREZ
    GENE
    ID GENE SYMBOL GENE DESCRIPTION
    1. 6348 CCL3 chemokine (C-C motif) ligand 3
    2. 200734 SPRED2 sprouty-related, EVH1 domain containing 2
    3. 117854 TRIM6 tripartite motif-containing 6
    4. 1846 DUSP4 dual specificity phosphatase 4
    5. 894 CCND2 cyclin D2
    6. 6241 RRM2 ribonucleotide reductase M2 polypeptide
    7. 4821 NKX2-2 NK2 transcription factor related, locus 2 (Drosophila)
    8. 3037 HAS2 hyaluronan synthase 2
    9. 990 CDC6 CDC6 cell division cycle 6 homolog (S. cerevisiae)
    10. 57405 SPBC25 spindle pole body component 25 homolog (S. cerevisiae)
    11. 934 CD24 CD24 antigen (small cell lung carcinoma cluster 4
    antigen)
    12. 55165 C10orf3 chromosome 10 open reading frame 3
    13. 55388 MCM10 MCM10 minichromosome maintenance deficient 10
    (S. cerevisiae)
    14. 79019 C22orf18 chromosome 22 open reading frame 18
    15. 9768 KIAA0101 KIAA0101
    16. 51659 Pfs2 DNA replication complex GINS protein PSF2
    17. 4605 MYBL2 v-myb myeloblastosis viral oncogene homolog
    (avian)-like 2
    18. 161742 SPRED1 sprouty-related, EVH1 domain containing 1
    19. 4175 MCM6 MCM6 minichromosome maintenance deficient 6
    (MIS5 homolog, S. pombe) (S. cerevisiae)
    20. 11130 ZWINT ZW10 interactor
    21. 26298 EHF ets homologous factor
    22. 7117 TMSL3 thymosin-like 3
    23. 890 CCNA2 cyclin A2
    24. 79075 DCC1 defective in sister chromatid cohesion homolog 1 (S. cerevisiae)
    25. 83879 CDCA7 cell division cycle associated 7
    26. 22873 DZIP1 DAZ interacting protein 1
    27. 51514 DTL denticleless homolog (Drosophila)
    28. 55789 DEPDC1B DEP domain containing 1B
    29. 55355 DKFZp762E1312 hypothetical protein DKFZp762E1312
    30. 10052 GJA7 gap junction protein, alpha 7, 45 kDa (connexin 45)
    31. 146909 LOC146909 hypothetical protein LOC146909
    32. 113130 CDCA5 cell division cycle associated 5
    33. 1017 CDK2 cyclin-dependent kinase 2
    34. 4176 MCM7 MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)
    35. 81610 C20orf129 chromosome 20 open reading frame 129
    36. 9833 MELK maternal embryonic leucine zipper kinase
    37. 29128 UHRF1 ubiquitin-like, containing PHD and RING finger
    domains, 1
    38. 4171 MCM2 MCM2 minichromosome maintenance deficient 2,
    mitotin (S. cerevisiae)
    39. 79801 SHCBP1 SHC SH2-domain binding protein 1
    40. 28231 SLCO4A1 solute carrier organic anion transporter family,
    member 4A1
    41. 113115 FAM54A family with sequence similarity 54, member A
    42. 22974 TPX2 TPX2, microtubule-associated protein homolog
    (Xenopus laevis)
    43. 9232 PTTG1 pituitary tumor-transforming 1
    44. 137392 LOC137392 similar to CG6405 gene product
    45. 195828 ZNF367 zinc finger protein 367
    46. 4288 MKI67 antigen identified by monoclonal antibody Ki-67
    47. 701 BUB1B BUB1 budding uninhibited by benzimidazoles 1
    homolog beta (yeast)
    48. 9928 KIF14 kinesin family member 14
    49. 3832 KIF11 kinesin family member 11
    50. 11065 UBE2C ubiquitin-conjugating enzyme E2C
    51. 9837 PSF1 DNA replication complex GINS protein PSF1
    52. 387103 C6orf173 chromosome 6 open reading frame 173
    53. 1870 E2F2 E2F transcription factor 2
    54. 79733 E2F8 E2F transcription factor 8
    55. 991 CDC20 CDC20 cell division cycle 20 homolog (S. cerevisiae)
    56. 3014 H2AFX H2A histone family, member X
    57. 10112 KIF20A kinesin family member 20A
    58. 993 CDC25A cell division cycle 25A
    59. 24137 KIF4A kinesin family member 4A
    60. 80144 FRAS1 Fraser syndrome 1
    61. 55010 FLJ20641 hypothetical protein FLJ20641
    62. 9319 TRIP13 thyroid hormone receptor interactor 13
    63. 9355 LHX2 LIM homeobox 2
    64. 7153 TOP2A topoisomerase (DNA) II alpha 170 kDa
    65. 4174 MCM5 MCM5 minichromosome maintenance deficient 5,
    cell division cycle 46 (S. cerevisiae)
    66. 55215 FLJ10719 hypothetical protein FLJ10719
    67. 11013 TMSL8 thymosin-like 8
    68. 5983 RFC3 replication factor C (activator 1) 3, 38 kDa
    69. 1063 CENPF centromere protein F, 350/400ka (mitosin)
    70. 3683 ITGAL integrin, alpha L (antigen CD11A (p180), lymphocyte
    function-associated antigen 1; alpha polypeptide)
    71. 2237 FEN1 flap structure-specific endonuclease 1
    72. 27338 UBE2S ubiquitin-conjugating enzyme E2S
    73. 4001 LMNB1 lamin B1
    74. 29089 UBE2T ubiquitin-conjugating enzyme E2T (putative)
    75. 55839 BM039 uncharacterized bone marrow protein BM039
    76. 2115 ETV1 ets variant gene 1
    77. 440279 UNC13C unc-13 homolog C (C. elegans)
    78. 962 CD48 CD48 antigen (B-cell membrane protein)
    79. 54910 SEMA4C sema domain, immunoglobulin domain (Ig),
    transmembrane domain (TM) and short cytoplasmic
    domain, (semaphorin) 4C
    80. 1902 EDG2 endothelial differentiation, lysophosphatidic acid G-
    protein-coupled receptor, 2
    81. 64946 CENPH centromere protein H
    82. 157570 ESCO2 establishment of cohesion 1 homolog 2 (S. cerevisiae)
    83. 389835 FAM72A family with sequence similarity 72, member A
    84. 144455 E2F7 E2F transcription factor 7
    85. 51512 GTSE1 G-2 and S-phase expressed 1
    86. 7298 TYMS thymidylate synthetase
    87. 7374 UNG uracil-DNA glycosylase
    88. 5578 PRKCA protein kinase C, alpha
    89. 672 BRCA1 breast cancer 1, early onset
    90. 84952 CGNL1 cingulin-like 1
    91. 10252 SPRY1 sprouty homolog 1, antagonist of FGF signaling
    (Drosophila)
    92. 79682 MLF1IP MLF1 interacting protein
    93. 8851 CDK5R1 cyclin-dependent kinase 5, regulatory subunit 1
    (p35)
    94. 10635 RAD51AP1 RAD51 associated protein 1
    95. 22998 KIAA1102 KIAA1102 protein
    96. 148203 LOC148203 hypothetical protein LOC148203
    97. 7465 WEE1 WEE1 homolog (S. pombe)
    98. 83540 CDCA1 cell division cycle associated 1
    99. 3070 HELLS helicase, lymphoid-specific
    100. 891 CCNB1 cyclin B1
    101. 6790 STK6 serine/threonine kinase 6
    102. 56992 KIF15 kinesin family member 15
    103. 7112 TMPO thymopoietin
    104. 63901 FLJ22794 FLJ22794 protein
    105. 9493 KIF23 kinesin family member 23
    106. 9133 CCNB2 cyclin B2
    107. 4173 MCM4 MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)
    108. 7083 TK1 thymidine kinase 1, soluble
    109. 983 CDC2 cell division cycle 2, G1 to S and G2 to M
    110. 11339 OIP5 Opa interacting protein 5
    111. 51203 NUSAP1 nucleolar and spindle associated protein 1
    112. 5111 PCNA proliferating cell nuclear antigen
    113. 11004 KIF2C kinesin family member 2C
    114. 54443 ANLN anillin, actin binding protein (scraps homolog,
    Drosophila)
    115. 83461 CDCA3 cell division cycle associated 3
    116. 4085 MAD2L1 MAD2 mitotic arrest deficient-like 1 (yeast)
    117. 9201 DCAMKL1 doublecortin and CaM kinase-like 1
    118. 1111 CHEK1 CHK1 checkpoint homolog (S. pombe)
    119. 9055 PRC1 protein regulator of cytokinesis 1
    120. 7804 LRP8 low density lipoprotein receptor-related protein 8,
    apolipoprotein e receptor
    121. 4915 NTRK2 neurotrophic tyrosine kinase, receptor, type 2
    122. 28951 TRIB2 tribbles homolog 2 (Drosophila)
    123. 4281 MID1 midline 1 (Opitz/BBB syndrome)
    124. 3148 HMGB2 high-mobility group box 2
    125. 3161 HMMR hyaluronan-mediated motility receptor (RHAMM)
    126. 10276 NET1 neuroepithelial cell transforming gene 1
    127. 29028 ATAD2 ATPase family, AAA domain containing 2
    128. 1062 CENPE centromere protein E, 312 kDa
    129. 1491 CTH cystathionase (cystathionine gamma-lyase)
    130. 10615 SPAG5 sperm associated antigen 5
    131. 64581 CLEC7A C-type lectin domain family 7, member A
    132. 10592 SMC2L1 SMC2 structural maintenance of chromosomes 2-
    like 1 (yeast)
    133. 332 BIRC5 baculoviral IAP repeat-containing 5 (survivin)
    134. 4172 MCM3 MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)
    135. 64105 FKSG14 leucine zipper protein FKSG14
    136. 64151 HCAP-G chromosome condensation protein G
    137. 1163 CKS1B CDC28 protein kinase regulatory subunit 1B
    138. 122769 PPIL5 peptidylprolyl isomerase (cyclophilin)-like 5
    139. 3398 ID2 inhibitor of DNA binding 2, dominant negative helix-
    loop-helix protein
    140. 22822 PHLDA1 pleckstrin homology-like domain, family A, member 1
    141. 1718 DHCR24 24-dehydrocholesterol reductase
    142. 145482 ZADH1 zinc binding alcohol dehydrogenase, domain
    containing 1
    143. 1847 DUSP5 dual specificity phosphatase 5
    144. 26271 FBXO5 F-box protein 5
    145. 9212 AURKB aurora kinase B
    146. 29968 PSAT1 phosphoserine aminotransferase 1
    147. 26147 PHF19 PHD finger protein 19
    148. 55635 DEPDC1 DEP domain containing 1
    149. 10403 KNTC2 kinetochore associated 2
    150. 64081 MAWBP MAWD binding protein
    151. 84858 ZNF503 zinc finger protein 503
    152. 55723 ASF1B ASF1 anti-silencing function 1 homolog B (S. cerevisiae)
    153. 7272 TTK TTK protein kinase
    154. 9535 GMFG glia maturation factor, gamma
    155. 1058 CENPA centromere protein A, 17 kDa
    156. 84515 MCM8 MCM8 minichromosome maintenance deficient 8 (S. cerevisiae)
    157. 54069 C21orf45 chromosome 21 open reading frame 45
    158. 5984 RFC4 replication factor C (activator 1) 4, 37 kDa
    159. 389831 LOC389831 hypothetical gene supported by AL713796
    160. 157313 CDCA2 cell division cycle associated 2
    161. 29127 RACGAP1 Rac GTPase activating protein 1
    162. 55872 PBK PDZ binding kinase
    163. 4678 NASP nuclear autoantigenic sperm protein (histone-
    binding)
    164. 7171 TPM4 tropomyosin 4
    165. 7443 VRK1 vaccinia related kinase 1
    166. 699 BUB1 BUB1 budding uninhibited by benzimidazoles 1
    homolog (yeast)
    167. 3925 STMN1 stathmin 1/oncoprotein 18
    168. 865 CBFB core-binding factor, beta subunit
    169. 399664 RKHD1 ring finger and KH domain containing 1
    170. 11168 PSIP1 PC4 and SFRS1 interacting protein 1
    171. 84057 GAJ GAJ protein
    172. 57082 CASC5 cancer susceptibility candidate 5
    173. 23286 KIBRA KIBRA protein
    174. 285513 LOC285513 hypothetical protein LOC285513
    175. 259266 ASPM asp (abnormal spindle)-like, microcephaly
    associated (Drosophila)
    176. 150468 FLJ40629 hypothetical protein FLJ40629
    177. 6659 SOX4 SRY (sex determining region Y)-box 4
    178. 51053 GMNN geminin, DNA replication inhibitor
    179. 3159 HMGA1 high mobility group AT-hook 1
    180. 81620 CDT1 DNA replication factor
    181. 11332 BACH brain acyl-CoA hydrolase
    182. 4751 NEK2 NIMA (never in mitosis gene a)-related kinase 2
    183. 1033 CDKN3 cyclin-dependent kinase inhibitor 3 (CDK2-
    associated dual specificity phosphatase)
    184. 8864 PER2 period homolog 2 (Drosophila)
    185. 3418 IDH2 isocitrate dehydrogenase 2 (NADP+), mitochondrial
    186. 63979 FIGNL1 fidgetin-like 1
    187. 55646 LYAR hypothetical protein FLJ20425
    188. 91614 LOC91614 novel 58.3 KDA protein
    189. 8630 HSD17B6 hydroxysteroid (17-beta) dehydrogenase 6
    190. 1038 CDR1 cerebellar degeneration-related protein 1, 34 kDa
    191. 6941 TCF19 transcription factor 19 (SC1)
    192. 256435 ST6GALNAC3 ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-
    1,3)-N-acetylgalactosaminide alpha-2,6-
    sialyltransferase 3
    193. 54892 LUZP5 leucine zipper protein 5
    194. 4603 MYBL1 v-myb myeloblastosis viral oncogene homolog
    (avian)-like 1
    195. 1719 DHFR dihydrofolate reductase
    196. 170954 KIAA1949 KIAA1949
    197. 7903 ST8SIA4 ST8 alpha-N-acetyl-neuraminide alpha-2,8-
    sialyltransferase 4
    198. 9787 DLG7 discs, large homolog 7 (Drosophila)
    199. 56935 FN5 FN5 protein
    200. 3015 H2AFZ H2A histone family, member Z
    201. 10189 THOC4 THO complex 4
    202. 494143 LOC494143 similar to RIKEN cDNA 2510006C20 gene
    203. 6240 RRM1 ribonucleotide reductase M1 polypeptide
    204. 1894 ECT2 epithelial cell transforming sequence 2 oncogene
    205. 7913 DEK DEK oncogene (DNA binding)
    206. 2146 EZH2 enhancer of zeste homolog 2 (Drosophila)
    207. 55055 FLJ10036 Zwilch
    208. 11073 TOPBP1 topoisomerase (DNA) II binding protein 1
    209. 55502 HES6 hairy and enhancer of split 6 (Drosophila)
    210. 55247 NEIL3 nei endonuclease VIII-like 3 (E. coli)
    211. 54885 FLJ20298 FLJ20298 protein
    212. 83641 C10orf45 chromosome 10 open reading frame 45
    213. 64919 BCL11B B-cell CLL/lymphoma 11B (zinc finger protein)
    214. 26095 PTPN20 protein tyrosine phosphatase, non-receptor type 20
    215. 23590 TPRT trans-prenyltransferase
    216. 387882 LOC387882 hypothetical protein
    217. 51232 CRIM1 cysteine-rich motor neuron 1
    218. 801 CALM1 calmodulin 1 (phosphorylase kinase, delta)
    219. 55964 SEPT3 septin 3
    220. 493861 EID3 E1A-like inhibitor of differentiation 3
    221. 29980 DONSON downstream neighbor of SON
    222. 147138 EVER2 epidermodysplasia verruciformis 2
    223. 80150 ASRGL1 asparaginase like 1
    224. 5985 RFC5 replication factor C (activator 1) 5, 36.5 kDa
    225. 51155 HN1 hematological and neurological expressed 1
    226. 7004 TEAD4 TEA domain family member 4
    227. 4325 MMP16 matrix metalloproteinase 16 (membrane-inserted)
    228. 203068 TUBB tubulin, beta polypeptide
    229. 4602 MYB v-myb myeloblastosis viral oncogene homolog
    (avian)
    230. 55706 TMEM48 transmembrane protein 48
    231. 348235 FAM33A family with sequence similarity 33, member A
    232. 8871 SYNJ2 synaptojanin 2
    233. 81563 C1orf21 chromosome 1 open reading frame 21
    234. 51192 CKLF chemokine-like factor
    235. 2326 FMO1 flavin containing monooxygenase 1
    236. 91057 NY-REN-41 NY-REN-41 antigen
    237. 10376 K-ALPHA-1 tubulin, alpha, ubiquitous
    238. 23234 DNAJC9 DnaJ (Hsp40) homolog, subfamily C, member 9
    239. 5982 RFC2 replication factor C (activator 1) 2, 40 kDa
    240. 51063 FAM26B family with sequence similarity 26, member B
    241. 9953 HS3ST3B1 heparan sulfate (glucosamine) 3-O-sulfotransferase
    3B1
    242. 79723 SUV39H2 suppressor of variegation 3-9 homolog 2
    (Drosophila)
    243. 79596 C13orf7 chromosome 13 open reading frame 7
    244. 23165 NUP205 nucleoporin 205 kDa
    245. 9530 BAG4 BCL2-associated athanogene 4
    246. 3146 HMGB1 high-mobility group box 1
    247. 445815 PALM2-AKAP2 PALM2-AKAP2 protein
    248. 5557 PRIM1 primase, polypeptide 1, 49 kDa
    249. 2983 GUCY1B3 guanylate cyclase 1, soluble, beta 3
    250. 51776 ZAK sterile alpha motif and leucine zipper containing
    kinase AZK
    251. 10926 ASK activator of S phase kinase
    252. 8833 GMPS guanine monphosphate synthetase
    253. 84930 MASTL microtubule associated serine/threonine kinase-like
    254. 90417 C15orf23 chromosome 15 open reading frame 23
    255. 8530 CST7 cystatin F (leukocystatin)
    256. 9532 BAG2 BCL2-associated athanogene 2
    257. 23310 hCAP-D3 KIAA0056 protein
    258. 283991 MGC29814 hypothetical protein MGC29814
    259. 91607 FLJ34922 hypothetical protein FLJ34922
    260. 7398 USP1 ubiquitin specific protease 1
    261. 2669 GEM GTP binding protein overexpressed in skeletal
    muscle
    262. 151246 SGOL2 shugoshin-like 2 (S. pombe)
    263. 23421 ITGB3BP integrin beta 3 binding protein (beta3-endonexin)
    264. 84969 C20orf100 chromosome 20 open reading frame 100
    265. 201725 LOC201725 hypothetical protein LOC201725
    266. 5361 PLXNA1 plexin A1
    267. 3708 ITPR1 inositol 1,4,5-triphosphate receptor, type 1
    268. 55740 ENAH enabled homolog (Drosophila)
    269. 126731 C1orf96 chromosome 1 open reading frame 96
    270. 57037 ANKMY2 ankyrin repeat and MYND domain containing 2
    271. 23331 KIAA1043 KIAA1043 protein
    272. 3930 LBR lamin B receptor
    273. 3838 KPNA2 karyopherin alpha 2 (RAG cohort 1, importin alpha
    1)
    274. 1230 CCR1 chemokine (C-C motif) receptor 1
    275. 2200 FBN1 fibrillin 1 (Marfan syndrome)
    276. 6867 TACC1 transforming, acidic coiled-coil containing protein 1
    277. 27115 PDE7B phosphodiesterase 7B
    278. 11151 CORO1A coronin, actin binding protein, 1A
    279. 6385 SDC4 syndecan 4 (amphiglycan, ryudocan)
    280. 3182 HNRPAB heterogeneous nuclear ribonucleoprotein A/B
    281. 5757 PTMA prothymosin, alpha (gene sequence 28)
    282. 83990 BRIP1 BRCA1 interacting protein C-terminal helicase 1
    283. 9830 TRIM14 tripartite motif-containing 14
    284. 57761 TRIB3 tribbles homolog 3 (Drosophila)
    285. 2026 ENO2 enolase 2 (gamma, neuronal)
    286. 8727 CTNNAL1 catenin (cadherin-associated protein), alpha-like 1
    287. 5880 RAC2 ras-related C3 botulinum toxin substrate 2 (rho
    family, small GTP binding protein Rac2)
    288. 864 RUNX3 runt-related transcription factor 3
    289. 10950 BTG3 BTG family, member 3
    290. 81539 SLC38A1 solute carrier family 38, member 1
    291. 26051 PPP1R16B protein phosphatase 1, regulatory (inhibitor) subunit
    16B
    292. 5793 PTPRG protein tyrosine phosphatase, receptor type, G
    293. 2767 GNA11 guanine nucleotide binding protein (G protein), alpha
    11 (Gq class)
    294. 55013 FLJ20647 hypothetical protein FLJ20647
    295. 4885 NPTX2 neuronal pentraxin II
    296. 79710 MORC4 MORC family CW-type zinc finger 4
    297. 490 ATP2B1 ATPase, Ca++ transporting, plasma membrane 1
    298. 2956 MSH6 mutS homolog 6 (E. coli)
    299. 6611 SMS spermine synthase
    300. 6627 SNRPA1 small nuclear ribonucleoprotein polypeptide A′
    301. 1434 CSE1L CSE1 chromosome segregation 1-like (yeast)
    302. 7371 UCK2 uridine-cytidine kinase 2
    303. 7277 TUBA1 tubulin, alpha 1 (testis specific)
    304. 1786 DNMT1 DNA (cytosine-5-)-methyltransferase 1
    305. 54801 FAM29A family with sequence similarity 29, member A
    306. 54908 FLJ20364 hypothetical protein FLJ20364
    307. 119467 MGC32871 hypothetical protein MGC32871
    308. 90390 THRAP6 thyroid hormone receptor associated protein 6
    309. 60468 BACH2 BTB and CNC homology 1, basic leucine zipper
    transcription factor 2
    310. 6510 SLC1A5 solute carrier family 1 (neutral amino acid
    transporter), member 5
    311. 6628 SNRPB small nuclear ribonucleoprotein polypeptides B and
    B1
    312. 205 AK3L1 adenylate kinase 3-like 1
    313. 116832 RPL39L ribosomal protein L39-like
    314. 79902 PCNT1 pericentrin 1
    315. 54962 FLJ20516 timeless-interacting protein
    316. 23279 NUP160 nucleoporin 160 kDa
    317. 23046 KIF21B kinesin family member 21B
    318. 2288 FKBP4 FK506 binding protein 4, 59 kDa
    319. 5698 PSMB9 proteasome (prosome, macropain) subunit, beta
    type, 9 (large multifunctional protease 2)
    320. 10160 FARP1 FERM, RhoGEF (ARHGEF) and pleckstrin domain
    protein 1 (chondrocyte-derived)
    321. 8502 PKP4 plakophilin 4
    322. 10675 CSPG5 chondroitin sulfate proteoglycan 5 (neuroglycan C)
    323. 29899 GPSM2 G-protein signalling modulator 2 (AGS3-like, C. elegans)
    324. 10602 CDC42EP3 CDC42 effector protein (Rho GTPase binding) 3
    325. 8243 SMC1L1 SMC1 structural maintenance of chromosomes 1-
    like 1 (yeast)
    326. 6347 CCL2 chemokine (C-C motif) ligand 2
    327. 5932 RBBP8 retinoblastoma binding protein 8
    328. 6877 TAF5 TAF5 RNA polymerase II, TATA box binding protein
    (TBP)-associated factor, 100 kDa
    329. 10801 SEPT9 septin 9
    330. 55536 CDCA7L cell division cycle associated 7-like
    331. 11340 EXOSC8 exosome component 8
    332. 5873 RAB27A RAB27A, member RAS oncogene family
    333. 53354 PANK1 pantothenate kinase 1
    334. 2534 FYN FYN oncogene related to SRC, FGR, YES
    335. 55166 C6orf139 chromosome 6 open reading frame 139
    336. 27346 MAC30 hypothetical protein MAC30
    337. 79037 MGC2463 hypothetical protein MGC2463
    338. 116496 C1orf24 chromosome 1 open reading frame 24
    339. 84314 MGC10744 hypothetical protein MGC10744
    340. 23531 MMD monocyte to macrophage differentiation-associated
    341. 6558 SLC12A2 solute carrier family 12 (sodium/potassium/chloride
    transporters), member 2
    342. 64282 PAPD5 PAP associated domain containing 5
    343. 55636 CHD7 chromodomain helicase DNA binding protein 7
    344. 55026 FLJ20716 hypothetical protein FLJ20716
    345. 22929 SEPHS1 selenophosphate synthetase 1
    346. 10541 ANP32B acidic (leucine-rich) nuclear phosphoprotein 32
    family, member B
    347. 79621 FLJ11712 hypothetical protein FLJ11712
    348. 6432 SFRS7 splicing factor, arginine/serine-rich 7, 35 kDa
    349. 5214 PFKP phosphofructokinase, platelet
    350. 26031 OSBPL3 oxysterol binding protein-like 3
    351. 1102 RCBTB2 regulator of chromosome condensation (RCC1) and
    BTB (POZ) domain containing protein 2
    352. 6929 TCF3 transcription factor 3 (E2A immunoglobulin enhancer
    binding factors E12/E47)
    353. 6632 SNRPD1 small nuclear ribonucleoprotein D1 polypeptide
    16 kDa
    354. 2047 EPHB1 EPH receptor B1
    355. 5168 ENPP2 ectonucleotide pyrophosphatase/phosphodiesterase
    2 (autotaxin)
    356. 55257 C20orf20 chromosome 20 open reading frame 20
    357. 81611 ANP32E acidic (leucine-rich) nuclear phosphoprotein 32
    family, member E
    358. 23246 BOP1 block of proliferation 1
    359. 23526 HA-1 minor histocompatibility antigen HA-1
    360. 84250 ANKRD32 ankyrin repeat domain 32
    361. 6999 TDO2 tryptophan 2,3-dioxygenase
    362. 8317 CDC7 CDC7 cell division cycle 7 (S. cerevisiae)
    363. 55752 SEPT11 septin 11
    364. 39 ACAT2 acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl
    Coenzyme A thiolase)
    365. 54830 FLJ20130 hypothetical protein FLJ20130
    366. 83732 RIOK1 RIO kinase 1 (yeast)
    367. 10808 HSPH1 heat shock 105 kDa/110 kDa protein 1
    368. 489 ATP2A3 ATPase, Ca++ transporting, ubiquitous
    369. 3251 HPRT1 hypoxanthine phosphoribosyltransferase 1 (Lesch-
    Nyhan syndrome)
    370. 10051 SMC4L1 SMC4 structural maintenance of chromosomes 4-
    like 1 (yeast)
    371. 55816 DOK5 docking protein 5
    372. 3676 ITGA4 integrin, alpha 4 (antigen CD49D, alpha 4 subunit of
    VLA-4 receptor)
    373. 8819 SAP30 sin3-associated polypeptide, 30 kDa
    374. 4436 MSH2 mutS homolog 2, colon cancer, nonpolyposis type 1
    (E. coli)
    375. 10212 DDX39 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39
    376. 5889 RAD51C RAD51 homolog C (S. cerevisiae)
    377. 134111 FLJ25076 similar to CG4502-PA
    378. 51377 UCHL5 ubiquitin carboxyl-terminal hydrolase L5
    379. 6657 SOX2 SRY (sex determining region Y)-box 2
    380. 241 ALOX5AP arachidonate 5-lipoxygenase-activating protein
    381. 79888 FLJ12443 hypothetical protein FLJ12443
    382. 1368 CPM carboxypeptidase M
    383. 397 ARHGDIB Rho GDP dissociation inhibitor (GDI) beta
    384. 3336 HSPE1 heat shock 10 kDa protein 1 (chaperonin 10)
    385. 2104 ESRRG estrogen-related receptor gamma
    386. 2171 FABP5 fatty acid binding protein 5 (psoriasis-associated)
    387. 6574 SLC20A1 solute carrier family 20 (phosphate transporter),
    member 1
    388. 2743 GLRB glycine receptor, beta
    389. 1019 CDK4 cyclin-dependent kinase 4
    390. 9295 SFRS11 splicing factor, arginine/serine-rich 11
    391. 56952 PRTFDC1 phosphoribosyl transferase domain containing 1
    392. 6472 SHMT2 serine hydroxymethyltransferase 2 (mitochondrial)
    393. 23512 SUZ12 suppressor of zeste 12 homolog (Drosophila)
    394. 586 BCAT1 branched chain aminotransferase 1, cytosolic
    395. 8836 GGH gamma-glutamyl hydrolase (conjugase,
    folylpolygammaglutamyl hydrolase)
    396. 10383 TUBB2 tubulin, beta, 2
    397. 54101 RIPK4 receptor-interacting serine-threonine kinase 4
    398. 130271 PLEKHH2 pleckstrin homology domain containing, family H
    (with MyTH4 domain) member 2
    399. 129401 NUP35 nucleoporin 35 kDa
    400. 10128 LRPPRC leucine-rich PPR-motif containing
    401. 51703 ACSL5 acyl-CoA synthetase long-chain family member 5
    402. 9448 MAP4K4 mitogen-activated protein kinase kinase kinase
    kinase 4
    403. 79017 C7orf24 chromosome 7 open reading frame 24
    404. 262 AMD1 adenosylmethionine decarboxylase 1
    405. 960 CD44 CD44 antigen (homing function and Indian blood
    group system)
    406. 81930 KIF18A kinesin family member 18A
    407. 64116 SLC39A8 solute carrier family 39 (zinc transporter), member 8
    408. 26586 CKAP2 cytoskeleton associated protein 2
    409. 51144 HSD17B12 hydroxysteroid (17-beta) dehydrogenase 12
    410. 51002 CGI-121 CGI-121 protein
    411. 9126 CSPG6 chondroitin sulfate proteoglycan 6 (bamacan)
    412. 79154 MGC4172 short-chain dehydrogenase/reductase
    413. 11096 ADAMTS5 a disintegrin-like and metalloprotease (reprolysin
    type) with thrombospondin type 1 motif, 5
    (aggrecanase-2)
    414. 84803 MGC11324 hypothetical protein MGC11324
    415. 4082 MARCKS myristoylated alanine-rich protein kinase C substrate
    416. 4086 SMAD1 SMAD, mothers against DPP homolog 1
    (Drosophila)
    417. 9446 GSTO1 glutathione S-transferase omega 1
    418. 23636 NUP62 nucleoporin 62 kDa
    419. 81839 VANGL1 vang-like 1 (van gogh, Drosophila)
    420. 3149 HMGB3 high-mobility group box 3
    421. 79023 NUP37 nucleoporin 37 kDa
    422. 10606 PAICS phosphoribosylaminoimidazole carboxylase,
    phosphoribosylaminoimidazole succinocarboxamide
    synthetase
    423. 10492 SYNCRIP synaptotagmin binding, cytoplasmic RNA interacting
    protein
    424. 3320 HSPCA heat shock 90 kDa protein 1, alpha
    425. 6119 RPA3 replication protein A3, 14 kDa
    426. 55352 HSA272196 hypothetical protein, clone 2746033
    427. 9759 HDAC4 histone deacetylase 4
    428. 5725 PTBP1 polypyrimidine tract binding protein 1
    429. 2119 ETV5 ets variant gene 5 (ets-related molecule)
    430. 10019 LNK lymphocyte adaptor protein
    431. 9734 HDAC9 histone deacetylase 9
    432. 5885 RAD21 RAD21 homolog (S. pombe)
    433. 79930 DOK3 docking protein 3
    434. 22837 COBLL1 COBL-like 1
    435. 339448 LOC339448 hypothetical protein LOC339448
    436. 11051 NUDT21 nudix (nucleoside diphosphate linked moiety X)-type
    motif 21
    437. 9735 KNTC1 kinetochore associated 1
    438. 4148 MATN3 matrilin 3
    439. 4200 ME2 malic enzyme 2, NAD(+)-dependent, mitochondrial
    440. 26084 SGEF Src homology 3 domain-containing guanine
    nucleotide exchange factor
    441. 27101 CACYBP calcyclin binding protein
    442. 23012 STK38L serine/threonine kinase 38 like
    443. 54566 EPB41L4B erythrocyte membrane protein band 4.1 like 4B
    444. 6566 SLC16A1 solute carrier family 16 (monocarboxylic acid
    transporters), member 1
    445. 54947 FLJ20481 hypothetical protein FLJ20481
    446. 255488 IBRDC2 IBR domain containing 2
    447. 2289 FKBP5 FK506 binding protein 5
    448. 5036 PA2G4 proliferation-associated 2G4, 38 kDa
    449. 4869 NPM1 nucleophosmin (nucleolar phosphoprotein B23,
    numatrin)
    450. 10384 BTN3A3 butyrophilin, subfamily 3, member A3
    451. 10785 WDR4 WD repeat domain 4
    452. 3099 HK2 hexokinase 2
    453. 56121 PCDHB15 protocadherin beta 15
    454. 10155 TRIM28 tripartite motif-containing 28
    455. 6340 SCNN1G sodium channel, nonvoltage-gated 1, gamma
    456. 25804 LSM4 LSM4 homolog, U6 small nuclear RNA associated
    (S. cerevisiae)
    457. 3939 LDHA lactate dehydrogenase A
    458. 57552 AADACL1 arylacetamide deacetylase-like 1
    459. 9184 BUB3 BUB3 budding uninhibited by benzimidazoles 3
    homolog (yeast)
    460. 657 BMPR1A bone morphogenetic protein receptor, type IA
    461. 5631 PRPS1 phosphoribosyl pyrophosphate synthetase 1
    462. 204 AK2 adenylate kinase 2
    463. 55270 NUDT15 nudix (nucleoside diphosphate linked moiety X)-type
    motif 15
    464. 10265 IRX5 iroquois homeobox protein 5
    465. 4640 MYO1A myosin IA
    466. 79180 EFHD2 EF hand domain family, member D2
    467. 4076 M11S1 membrane component, chromosome 11, surface
    marker 1
    468. 55276 PGM2 phosphoglucomutase 2
    469. 83857 ARG99 ARG99 protein
    470. 116448 OLIG1 oligodendrocyte transcription factor 1
    471. 5696 PSMB8 proteasome (prosome, macropain) subunit, beta
    type, 8 (large multifunctional protease 7)
    472. 1407 CRY1 cryptochrome 1 (photolyase-like)
    473. 11177 BAZ1A bromodomain adjacent to zinc finger domain, 1A
    474. 51015 ISOC1 isochorismatase domain containing 1
    475. 1789 DNMT3B DNA (cytosine-5-)-methyltransferase 3 beta
    476. 22948 CCT5 chaperonin containing TCP1, subunit 5 (epsilon)
    477. 158563 LOC158563 hypothetical protein LOC158563
    478. 89891 WDR34 WD repeat domain 34
    479. 119 ADD2 adducin 2 (beta)
    480. 5358 PLS3 plastin 3 (T isoform)
    481. 7086 TKT transketolase (Wernicke-Korsakoff syndrome)
    482. 51174 TUBD1 tubulin, delta 1
    483. 23255 KIAA0802 KIAA0802
    484. 54149 C21orf91 chromosome 21 open reading frame 91
    485. 2271 FH fumarate hydratase
    486. 55076 TMEM45A transmembrane protein 45A
    487. 10436 C2F C2f protein
    488. 8553 BHLHB2 basic helix-loop-helix domain containing, class B, 2
    489. 10409 BASP1 brain abundant, membrane attached signal protein 1
    490. 22856 CHSY1 carbohydrate (chondroitin) synthase 1
    491. 84451 KIAA1804 mixed lineage kinase 4
    492. 3150 HMGN1 high-mobility group nucleosome binding domain 1
    493. 961 CD47 CD47 antigen (Rh-related antigen, integrin-
    associated signal transducer)
    494. 79038 ZFYVE21 zinc finger, FYVE domain containing 21
    495. 7291 TWIST1 twist homolog 1 (acrocephalosyndactyly 3; Saethre-
    Chotzen syndrome) (Drosophila)
    496. 9738 CP110 CP110 protein
    497. 10625 IVNS1ABP influenza virus NS1A binding protein
    498. 9368 SLC9A3R1 solute carrier family 9 (sodium/hydrogen exchanger),
    isoform 3 regulator 1
    499. 3613 IMPA2 inositol(myo)-1(or 4)-monophosphatase 2
    500. 8514 KCNAB2 potassium voltage-gated channel, shaker-related
    subfamily, beta member 2
    501. 4957 ODF2 outer dense fiber of sperm tails 2
    502. 4673 NAP1L1 nucleosome assembly protein 1-like 1
    503. 26018 LRIG1 leucine-rich repeats and immunoglobulin-like
    domains 1
    504. 3033 HADHSC L-3-hydroxyacyl-Coenzyme A dehydrogenase, short
    chain
    505. 139886 LOC139886 hypothetical protein LOC139886
    506. 10360 NPM3 nucleophosmin/nucleoplasmin, 3
    507. 200894 ARL2L1 ADP-ribosylation factor-like 2-like 1
    508. 8364 HIST1H4C histone 1, H4c
    509. 378708 APITD1 apoptosis-inducing, TAF9-like domain 1
    510. 169270 ZNF596 zinc finger protein 596
    511. 6917 TCEA1 transcription elongation factor A (SII), 1
    512. 7091 TLE4 transducin-like enhancer of split 4 (E(sp1) homolog,
    Drosophila)
    513. 3725 JUN v-jun sarcoma virus 17 oncogene homolog (avian)
    514. 1736 DKC1 dyskeratosis congenita 1, dyskerin
    515. 8566 PDXK pyridoxal (pyridoxine, vitamin B6) kinase
    516. 51176 LEF1 lymphoid enhancer-binding factor 1
    517. 87 ACTN1 actinin, alpha 1
    518. 10838 ZNF275 zinc finger protein 275
    519. 54517 FLJ20485 hypothetical protein FLJ20485
    520. 5150 PDE7A phosphodiesterase 7A
    521. 384 ARG2 arginase, type II
    522. 27316 RBMX RNA binding motif protein, X-linked
    523. 389206 CCDC4 coiled-coil domain containing 4
    524. 51312 SLC25A37 solute carrier family 25, member 37
    525. 9112 MTA1 metastasis associated 1
    526. 6711 SPTBN1 spectrin, beta, non-erythrocytic 1
    527. 10129 13CDNA73 hypothetical protein CG003
    528. 80014 BOMB BH3-only member B protein
    529. 27131 SNX5 sorting nexin 5
    530. 23089 PEG10 paternally expressed 10
    531. 5270 SERPINE2 serine (or cysteine) proteinase inhibitor, clade E
    (nexin, plasminogen activator inhibitor type 1),
    member 2
    532. 6764 ST5 suppression of tumorigenicity 5
    533. 7791 ZYX zyxin
    534. 22995 Cep152 KIAA0912 protein
    535. 4137 MAPT microtubule-associated protein tau
    536. 5411 PNN pinin, desmosome associated protein
    537. 3087 HHEX hematopoietically expressed homeobox
    538. 23171 GPD1L glycerol-3-phosphate dehydrogenase 1-like
    539. 56905 DKFZP434H132 DKFZP434H132 protein
    540. 3189 HNRPH3 heterogeneous nuclear ribonucleoprotein H3 (2H9)
    541. 9099 USP2 ubiquitin specific protease 2
    542. 10098 TSPAN5 tetraspanin 5
    543. 401505 C9orf105 chromosome 9 open reading frame 105
    544. 51444 RNF138 ring finger protein 138
    545. 11118 BTN3A2 butyrophilin, subfamily 3, member A2
    546. 8089 YEATS4 YEATS domain containing 4
    547. 84108 PCGF6 polycomb group ring finger 6
    548. 7514 XPO1 exportin 1 (CRM1 homolog, yeast)
    549. 9818 NUPL1 nucleoporin like 1
    550. 10923 PC4 activated RNA polymerase II transcription cofactor 4
    551. 6526 SLC5A3 solute carrier family 5 (inositol transporters),
    member 3
    552. 26010 DNAPTP6 DNA polymerase-transactivated protein 6
    553. 5307 PITX1 paired-like homeodomain transcription factor 1
    554. 2643 GCH1 GTP cyclohydrolase 1 (dopa-responsive dystonia)
    555. 1503 CTPS CTP synthase
    556. 5777 PTPN6 protein tyrosine phosphatase, non-receptor type 6
    557. 23122 CLASP2 cytoplasmic linker associated protein 2
    558. 5588 PRKCQ protein kinase C, theta
    559. 64770 CCDC14 coiled-coil domain containing 14
    560. 6426 SFRS1 splicing factor, arginine/serine-rich 1 (splicing factor
    2, alternate splicing factor)
    561. 81831 NETO2 neuropilin (NRP) and tolloid (TLL)-like 2
    562. 56888 KCMF1 potassium channel modulatory factor 1
    563. 9221 NOLC1 nucleolar and coiled-body phosphoprotein 1
    564. 79366 NSBP1 nucleosomal binding protein 1
    565. 51729 WBP11 WW domain binding protein 11
    566. 84444 DOT1L DOT1-like, histone H3 methyltransferase (S. cerevisiae)
    567. 80218 MAK3 Mak3 homolog (S. cerevisiae)
    568. 84319 MGC4308 hypothetical protein MGC4308
    569. 112479 MGC16943 similar to RIKEN cDNA 4933424N09 gene
    570. 64396 GMCL1L germ cell-less homolog 1 (Drosophila)-like
    571. 5905 RANGAP1 Ran GTPase activating protein 1
    572. 2177 FANCD2 Fanconi anemia, complementation group D2
    573. 55632 KIAA1333 KIAA1333
    574. 3695 ITGB7 integrin, beta 7
    575. 9793 CKAP5 cytoskeleton associated protein 5
    576. 5318 PKP2 plakophilin 2
    577. 6652 SORD sorbitol dehydrogenase
    578. 80709 AKNA AT-hook transcription factor
    579. 55120 FANCL Fanconi anemia, complementation group L
    580. 92667 C20orf72 chromosome 20 open reading frame 72
    581. 3654 IRAK1 interleukin-1 receptor-associated kinase 1
    582. 55975 KLHL7 kelch-like 7 (Drosophila)
    583. 6397 SEC14L1 SEC14-like 1 (S. cerevisiae)
    584. 29117 BRD7 bromodomain containing 7
    585. 6732 SRPK1 SFRS protein kinase 1
    586. 401081 FLJ22763 hypothetical gene supported by AK026416
    587. 8520 HAT1 histone acetyltransferase 1
    588. 3119 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1
    589. 7283 TUBG1 tubulin, gamma 1
    590. 4809 NHP2L1 NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae)
    591. 2778 GNAS GNAS complex locus
    592. 5359 PLSCR1 phospholipid scramblase 1
    593. 196294 FLJ25059 hypothetical protein FLJ25059
    594. 3181 HNRPA2B1 heterogeneous nuclear ribonucleoprotein A2/B1
    595. 1794 DOCK2 dedicator of cytokinesis 2
    596. 55148 C14orf130 chromosome 14 open reading frame 130
    597. 25924 MYRIP myosin VIIA and Rab interacting protein
    598. 7533 YWHAH tyrosine 3-monooxygenase/tryptophan 5-
    monooxygenase activation protein, eta polypeptide
    599. 64968 MRPS6 mitochondrial ribosomal protein S6
    600. 4830 NME1 non-metastatic cells 1, protein (NM23A) expressed
    in
    601. 165055 FLJ32745 hypothetical protein FLJ32745
    602. 151827 LRRC34 leucine rich repeat containing 34
    603. 93081 LOC93081 hypothetical protein BC015148
    604. 196527 TMEM16F transmembrane protein 16F
    605. 1827 DSCR1 Down syndrome critical region gene 1
    606. 203562 TMEM31 transmembrane protein 31
    607. 11335 CBX3 chromobox homolog 3 (HP1 gamma homolog,
    Drosophila)
    608. 3662 IRF4 interferon regulatory factor 4
    609. 8624 DSCR2 Down syndrome critical region gene 2
    610. 4092 SMAD7 SMAD, mothers against DPP homolog 7
    (Drosophila)
    611. 6934 TCF7L2 transcription factor 7-like 2 (T-cell specific, HMG-
    box)
    612. 26112 DKFZP434C171 DKFZP434C171 protein
    613. 3329 HSPD1 heat shock 60 kDa protein 1 (chaperonin)
    614. 5577 PRKAR2B protein kinase, cAMP-dependent, regulatory, type II,
    beta
    615. 3202 HOXA5 homeo box A5
    616. 79442 LRRC2 leucine rich repeat containing 2
    617. 9631 NUP155 nucleoporin 155 kDa
    618. 55366 LGR4 leucine-rich repeat-containing G protein-coupled
    receptor 4
    619. 23350 SR140 U2-associated SR140 protein
    620. 6434 SFRS10 splicing factor, arginine/serine-rich 10 (transformer 2
    homolog, Drosophila)
    621. 7975 MAFK v-maf musculoaponeurotic fibrosarcoma oncogene
    homolog K (avian)
    622. 3187 HNRPH1 heterogeneous nuclear ribonucleoprotein H1 (H)
    623. 94239 H2AFV H2A histone family, member V
    624. 54913 RPP25 ribonuclease P 25 kDa subunit
    625. 9521 EEF1E1 eukaryotic translation elongation factor 1 epsilon 1
    626. 5471 PPAT phosphoribosyl pyrophosphate amidotransferase
    627. 340252 ZNF680 zinc finger protein 680
    628. 1021 CDK6 cyclin-dependent kinase 6
    629. 10560 SLC19A2 solute carrier family 19 (thiamine transporter),
    member 2
    630. 4201 MEA1 male-enhanced antigen 1
    631. 440145 LOC440145 similar to RIKEN cDNA 2410129H14
    632. 3843 RANBP5 RAN binding protein 5
    633. 3298 HSF2 heat shock transcription factor 2
    634. 387914 TMEM46 transmembrane protein 46
    635. 27347 STK39 serine threonine kinase 39 (STE20/SPS1 homolog,
    yeast)
    636. 6256 RXRA retinoid X receptor, alpha
    637. 6637 SNRPG small nuclear ribonucleoprotein polypeptide G
    638. 22800 RRAS2 related RAS viral (r-ras) oncogene homolog 2
    639. 91694 FLJ23749 hypothetical protein FLJ23749
    640. 22823 MTF2 metal response element binding transcription factor 2
    641. 51184 MGC14560 protein x 0004
    642. 10856 RUVBL2 RuvB-like 2 (E. coli)
    643. 7188 TRAF5 TNF receptor-associated factor 5
    644. 5272 SERPINB9 serine (or cysteine) proteinase inhibitor, clade B
    (ovalbumin), member 9
    645. 11169 WDHD1 WD repeat and HMG-box DNA binding protein 1
    646. 5606 MAP2K3 mitogen-activated protein kinase kinase 3
    647. 4783 NFIL3 nuclear factor, interleukin 3 regulated
    648. 51691 LSM8 LSM8 homolog, U6 small nuclear RNA associated
    (S. cerevisiae)
    649. 1528 CYB5 cytochrome b-5
    650. 79899 FLJ14213 hypothetical protein FLJ14213
    651. 7334 UBE2N ubiquitin-conjugating enzyme E2N (UBC13
    homolog, yeast)
    652. 2730 GCLM glutamate-cysteine ligase, modifier subunit
    653. 23157 SEPT6 septin 6
    654. 56155 TEX14 testis expressed sequence 14
    655. 23658 LSM5 LSM5 homolog, U6 small nuclear RNA associated
    (S. cerevisiae)
    656. 1400 CRMP1 collapsin response mediator protein 1
    657. 5684 PSMA3 proteasome (prosome, macropain) subunit, alpha
    type, 3
    658. 6713 SQLE squalene epoxidase
    659. 84955 NUDCD1 NudC domain containing 1
    660. 64318 C10orf117 chromosome 10 open reading frame 117
    661. 10196 HRMT1L3 HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)
    662. 29841 GRHL1 grainyhead-like 1 (Drosophila)
    663. 10055 SAE1 SUMO-1 activating enzyme subunit 1
    664. 9214 FAIM3 Fas apoptotic inhibitory molecule 3
    665. 57406 ABHD6 abhydrolase domain containing 6
    666. 25914 RTTN rotatin
    667. 23244 SCC-112 SCC-112 protein
    668. 3183 HNRPC heterogeneous nuclear ribonucleoprotein C (C1/C2)
    669. 55117 SLC6A15 solute carrier family 6, member 15
    670. 6950 TCP1 t-complex 1
    671. 4660 PPP1R12B protein phosphatase 1, regulatory (inhibitor) subunit
    12B
    672. 134429 STARD4 START domain containing 4, sterol regulated
    673. 157503 LOC157503 hypothetical protein LOC157503
    674. 253832 ZDHHC20 zinc finger, DHHC-type containing 20
    675. 375061 MGC15887 hypothetical gene supported by BC009447
    676. 84986 ARHGAP19 Rho GTPase activating protein 19
    677. 8407 TAGLN2 transgelin 2
    678. 285704 RGMB RGM domain family, member B
    679. 5050 PAFAH1B3 platelet-activating factor acetylhydrolase, isoform Ib,
    gamma subunit 29 kDa
    680. 4208 MEF2C MADS box transcription enhancer factor 2,
    polypeptide C (myocyte enhancer factor 2C)
    681. 55614 C20orf23 chromosome 20 open reading frame 23
    682. 388796 LOC388796 hypothetical LOC388796
    683. 85463 ZC3H12C zinc finger CCCH-type containing 12C
    684. 51465 UBE2J1 ubiquitin-conjugating enzyme E2, J1 (UBC6
    homolog, yeast)
    685. 9994 CASP8AP2 CASP8 associated protein 2
    686. 26135 PAI-RBP1 PAI-1 mRNA binding protein
    687. 5634 PRPS2 phosphoribosyl pyrophosphate synthetase 2
    688. 286319 TUSC1 tumor suppressor candidate 1
    689. 6470 SHMT1 serine hydroxymethyltransferase 1 (soluble)
    690. 9397 NMT2 N-myristoyltransferase 2
    691. 10762 NUP50 nucleoporin 50 kDa
    692. 201161 PRR6 proline rich 6
    693. 5019 OXCT1 3-oxoacid CoA transferase 1
    694. 159 ADSS adenylosuccinate synthase
    695. 23587 DERP6 S-phase 2 protein
    696. 10151 HNRPA3P1 heterogeneous nuclear ribonucleoprotein A3
    pseudogene 1
    697. 8564 KMO kynurenine 3-monooxygenase (kynurenine 3-
    hydroxylase)
    698. 1349 COX7B cytochrome c oxidase subunit VIIb
    699. 283824 LOC283824 hypothetical protein LOC283824
    700. 1123 CHN1 chimerin (chimaerin) 1
    701. 57522 SRGAP1 SLIT-ROBO Rho GTPase activating protein 1
    702. 253782 LASS6 LAG1 longevity assurance homolog 6 (S. cerevisiae)
    703. 57685 KIAA1573 KIAA1573 protein
    704. 79695 GALNT12 UDP-N-acetyl-alpha-D-galactosamine:polypeptide
    N-acetylgalactosaminyltransferase 12 (GalNAc-T12)
    705. 90861 C16orf34 chromosome 16 open reading frame 34
    706. 26207 PITPNC1 phosphatidylinositol transfer protein, cytoplasmic 1
    707. 1164 CKS2 CDC28 protein kinase regulatory subunit 2
    708. 396 ARHGDIA Rho GDP dissociation inhibitor (GDI) alpha
    709. 57530 CGN cingulin
    710. 1633 DCK deoxycytidine kinase
    711. 9208 LRRFIP1 leucine rich repeat (in FLII) interacting protein 1
    712. 6453 ITSN1 intersectin 1 (SH3 domain protein)
    713. 24147 FJX1 four jointed box 1 (Drosophila)
    714. 9882 TBC1D4 TBC1 domain family, member 4
    715. 169200 DKFZp762C1112 hypothetical protein DKFZp762C1112
    716. 9331 B4GALT6 UDP-Gal:betaGlcNAc beta 1,4-
    galactosyltransferase, polypeptide 6
    717. 55183 RIF1 RAP1 interacting factor homolog (yeast)
    718. 221362 LOC221362 hypothetical protein LOC221362
    719. 8458 TTF2 transcription termination factor, RNA polymerase II
    720. 1047 CLGN calmegin
    721. 56919 DHX33 DEAH (Asp-Glu-Ala-His) box polypeptide 33
    722. 93949 CXorf10 chromosome X open reading frame 10
    723. 5569 PKIA protein kinase (cAMP-dependent, catalytic) inhibitor
    alpha
    724. 6891 TAP2 transporter 2, ATP-binding cassette, sub-family B
    (MDR/TAP)
    725. 1960 EGR3 early growth response 3
    726. 11252 PACSIN2 protein kinase C and casein kinase substrate in
    neurons 2
    727. 51762 RAB8B RAB8B, member RAS oncogene family
    728. 81575 DKFZP434F0318 hypothetical protein DKFZp434F0318
    729. 56906 THAP10 THAP domain containing 10
    730. 55110 FLJ10292 mago-nashi homolog
    731. 5267 SERPINA4 serine (or cysteine) proteinase inhibitor, clade A
    (alpha-1 antiproteinase, antitrypsin), member 4
    732. 1844 DUSP2 dual specificity phosphatase 2
    733. 9612 NCOR2 nuclear receptor co-repressor 2
    734. 3276 HRMT1L2 HMT1 hnRNP methyltransferase-like 2 (S. cerevisiae)
    735. 257415 MGC40405 hypothetical protein MGC40405
    736. 79720 FLJ12750 hypothetical protein FLJ12750
    737. 160897 ITR intimal thickness-related receptor
    738. 4522 MTHFD1 methylenetetrahydrofolate dehydrogenase (NADP+
    dependent) 1, methenyltetrahydrofolate
    cyclohydrolase, formyltetrahydrofolate synthetase
    739. 4668 NAGA N-acetylgalactosaminidase, alpha-
    740. 84890 C10orf22 chromosome 10 open reading frame 22
    741. 5198 PFAS phosphoribosylformylglycinamidine synthase (FGAR
    amidotransferase)
    742. 55544 RNPC1 RNA-binding region (RNP1, RRM) containing 1
    743. 2618 GART phosphoribosylglycinamide formyltransferase,
    phosphoribosylglycinamide synthetase,
    phosphoribosylaminoimidazole synthetase
    744. 9261 MAPKAPK2 mitogen-activated protein kinase-activated protein
    kinase 2
    745. 285761 DCBLD1 discoidin, CUB and LCCL domain containing 1
    746. 23225 NUP210 nucleoporin 210 kDa
    747. 9792 SERTAD2 SERTA domain containing 2
    748. 56938 ARNTL2 aryl hydrocarbon receptor nuclear translocator-like 2
    749. 23254 KIAA1026 kazrin
    750. 4628 MYH10 myosin, heavy polypeptide 10, non-muscle
    751. 23176 SEPT8 septin 8
    752. 1432 MAPK14 mitogen-activated protein kinase 14
    753. 84549 RBM13 RNA binding motif protein 13
    754. 84133 ZNRF3 zinc and ring finger 3
    755. 6502 SKP2 S-phase kinase-associated protein 2 (p45)
    756. 59274 MESDC1 mesoderm development candidate 1
    757. 51496 HSPC129 hypothetical protein HSPC129
    758. 55151 TMEM38B transmembrane protein 38B
    759. 57609 KIAA1463 KIAA1463 protein
    760. 1039 CDR2 cerebellar degeneration-related protein 2, 62 kDa
    761. 143098 MPP7 membrane protein, palmitoylated 7 (MAGUK p55
    subfamily member 7)
    762. 130589 GALM galactose mutarotase (aldose 1-epimerase)
    763. 3937 LCP2 lymphocyte cytosolic protein 2 (SH2 domain
    containing leukocyte protein of 76 kDa)
    764. 5420 PODXL podocalyxin-like
    765. 6509 SLC1A4 solute carrier family 1 (glutamate/neutral amino acid
    transporter), member 4
    766. 64397 ZFP106 zinc finger protein 106 homolog (mouse)
    767. 4860 NP nucleoside phosphorylase
    768. 3535 IGL@ immunoglobulin lambda locus
    769. 1396 CRIP1 cysteine-rich protein 1 (intestinal)
    770. 1660 DHX9 DEAH (Asp-Glu-Ala-His) box polypeptide 9
    771. 4291 MLF1 myeloid leukemia factor 1
    772. 26973 CHORDC1 cysteine and histidine-rich domain (CHORD)-
    containing, zinc binding protein 1
    773. 81037 CRR9 cisplatin resistance related protein CRR9p
    774. 10574 CCT7 chaperonin containing TCP1, subunit 7 (eta)
    775. 79892 C10orf119 chromosome 10 open reading frame 119
    776. 9972 NUP153 nucleoporin 153 kDa
    777. 10459 MAD2L2 MAD2 mitotic arrest deficient-like 2 (yeast)
    778. 483 ATP1B3 ATPase, Na+/K+ transporting, beta 3 polypeptide
    779. 7552 ZNF6 zinc finger protein 6 (CMPX1)
    780. 8165 AKAP1 A kinase (PRKA) anchor protein 1
    781. 29097 CNIH4 cornichon homolog 4 (Drosophila)
    782. 11198 SUPT16H suppressor of Ty 16 homolog (S. cerevisiae)
    783. 2184 FAH fumarylacetoacetate hydrolase
    (fumarylacetoacetase)
    784. 7037 TFRC transferrin receptor (p90, CD71)
    785. 6461 SHB Src homology 2 domain containing adaptor protein B
    786. 509 ATP5C1 ATP synthase, H+ transporting, mitochondrial F1
    complex, gamma polypeptide 1
    787. 5591 PRKDC protein kinase, DNA-activated, catalytic polypeptide
    788. 10682 EBP emopamil binding protein (sterol isomerase)
    789. 9188 DDX21 DEAD (Asp-Glu-Ala-Asp) box polypeptide 21
    790. 3837 KPNB1 karyopherin (importin) beta 1
    791. 3191 HNRPL heterogeneous nuclear ribonucleoprotein L
    792. 10236 HNRPR heterogeneous nuclear ribonucleoprotein R
    793. 6907 TBL1X transducin (beta)-like 1X-linked
    794. 56172 ANKH ankylosis, progressive homolog (mouse)
    795. 23367 LARP1 La ribonucleoprotein domain family, member 1
    796. 5778 PTPN7 protein tyrosine phosphatase, non-receptor type 7
    797. 100 ADA adenosine deaminase
    798. 2821 GPI glucose phosphate isomerase
    799. 9697 TRAM2 translocation associated membrane protein 2
    800. 54927 CHCHD3 coiled-coil-helix-coiled-coil-helix domain containing 3
    801. 58478 MASA E-1 enzyme
    802. 6322 SCML1 sex comb on midleg-like 1 (Drosophila)
    803. 292 SLC25A5 solute carrier family 25 (mitochondrial carrier;
    adenine nucleotide translocator), member 5
    804. 10857 PGRMC1 progesterone receptor membrane component 1
    805. 55342 STRBP spermatid perinuclear RNA binding protein
    806. 7150 TOP1 topoisomerase (DNA) I
    807. 874 CBR3 carbonyl reductase 3
    808. 51096 WDR50 WD repeat domain 50
    809. 253558 LYCAT lysocardiolipin acyltransferase
    810. 79053 ALG8 asparagine-linked glycosylation 8 homolog (yeast,
    alpha-1,3-glucosyltransferase)
    811. 84300 C6orf125 chromosome 6 open reading frame 125
    812. 8975 USP13 ubiquitin specific protease 13 (isopeptidase T-3)
    813. 220988 HNRPA3 heterogeneous nuclear ribonucleoprotein A3
    814. 5315 PKM2 pyruvate kinase, muscle
    815. 7411 VBP1 von Hippel-Lindau binding protein 1
    816. 1665 DHX15 DEAH (Asp-Glu-Ala-His) box polypeptide 15
    817. 10963 STIP1 stress-induced-phosphoprotein 1 (Hsp70/Hsp90-
    organizing protein)
    818. 253461 ZBTB38 zinc finger and BTB domain containing 38
    819. 29080 HSPC128 HSPC128 protein
    820. 84275 MGC4399 mitochondrial carrier protein
    821. 1622 DBI diazepam binding inhibitor (GABA receptor
    modulator, acyl-Coenzyme A binding protein)
    822. 4953 ODC1 ornithine decarboxylase 1
    823. 2029 ENSA endosulfine alpha
    824. 6404 SELPLG selectin P ligand
    825. 81034 MFTC mitochondrial folate transporter/carrier
    826. 81542 TXNDC thioredoxin domain containing
    827. 25816 TNFAIP8 tumor necrosis factor, alpha-induced protein 8
    828. 51582 AZIN1 antizyme inhibitor 1
    829. 27436 EML4 echinoderm microtubule associated protein like 4
    830. 55720 FLJ10534 hypothetical protein FLJ10534
    831. 7295 TXN thioredoxin
    832. 10539 TXNL2 thioredoxin-like 2
    833. 86 ACTL6A actin-like 6A
    834. 6731 SRP72 signal recognition particle 72 kDa
    835. 23314 SATB2 SATB family member 2
    836. 2273 FHL1 four and a half LIM domains 1
    837. 3422 IDI1 isopentenyl-diphosphate delta isomerase
    838. 10935 PRDX3 peroxiredoxin 3
    839. 2958 GTF2A2 general transcription factor IIA, 2, 12 kDa
    840. 4144 MAT2A methionine adenosyltransferase II, alpha
    841. 1964 EIF1AX eukaryotic translation initiation factor 1A, X-linked
    842. 60 ACTB actin, beta
    843. 11191 PTENP1 phosphatase and tensin homolog (mutated in
    multiple advanced cancers 1), pseudogene 1
    844. 90843 TCEAL8 transcription elongation factor A (SII)-like 8
    845. 57181 SLC39A10 solute carrier family 39 (zinc transporter), member
    10
    846. 11147 HHLA3 HERV-H LTR-associating 3
    847. 10553 HTATIP2 HIV-1 Tat interactive protein 2, 30 kDa
    848. 3338 DNAJC4 DnaJ (Hsp40) homolog, subfamily C, member 4
    849. 84888 SPPL2A signal peptide peptidase-like 2A
    850. 1955 EGFL5 EGF-like-domain, multiple 5
    851. 329 BIRC2 baculoviral IAP repeat-containing 2
    852. 29927 SEC61A1 Sec61 alpha 1 subunit (S. cerevisiae)
    853. 9559 VPS26 vacuolar protein sorting 26 (yeast)
    854. 23270 TSPYL4 TSPY-like 4
    855. 6309 SC5DL sterol-C5-desaturase (ERG3 delta-5-desaturase
    homolog, fungal)-like
    856. 10397 NDRG1 N-myc downstream regulated gene 1
    857. 27032 ATP2C1 ATPase, Ca++ transporting, type 2C, member 1
    858. 11112 HIBADH 3-hydroxyisobutyrate dehydrogenase
    859. 1476 CSTB cystatin B (stefin B)
    860. 9620 CELSR1 cadherin, EGF LAG seven-pass G-type receptor 1
    (flamingo homolog, Drosophila)
    861. 56650 C3orf4 chromosome 3 open reading frame 4
    862. 29922 NME7 non-metastatic cells 7, protein expressed in
    (nucleoside-diphosphate kinase)
    863. 8887 TAX1BP1 Tax1 (human T-cell leukemia virus type I) binding
    protein 1
    864. 5445 PON2 paraoxonase 2
    865. 81889 FAHD1 fumarylacetoacetate hydrolase domain containing 1
    866. 694 BTG1 B-cell translocation gene 1, anti-proliferative
    867. 29058 C20orf30 chromosome 20 open reading frame 30
    868. 2752 GLUL glutamate-ammonia ligase (glutamine synthase)
    869. 79717 FLJ11838 hypothetical protein FLJ11838
    870. 170622 COMMD6 COMM domain containing 6
    871. 5792 PTPRF protein tyrosine phosphatase, receptor type, F
    872. 64393 WIG1 p53 target zinc finger protein
    873. 549 AUH AU RNA binding protein/enoyl-Coenzyme A
    hydratase
    874. 51282 SCAND1 SCAN domain containing 1
    875. 79027 ZNF655 zinc finger protein 655
    876. 6451 SH3BGRL SH3 domain binding glutamic acid-rich protein like
    877. 1347 COX7A2 cytochrome c oxidase subunit VIIa polypeptide 2
    (liver)
    878. 550643 LOC550643 hypothetical protein LOC550643
    879. 6926 TBX3 T-box 3 (ulnar mammary syndrome)
    880. 51614 SDBCAG84 serologically defined breast cancer antigen 84
    881. 9520 NPEPPS aminopeptidase puromycin sensitive
    882. 51065 RPS27L ribosomal protein S27-like
    883. 10116 FEM1B fem-1 homolog b (C. elegans)
    884. 10521 DDX17 DEAD (Asp-Glu-Ala-Asp) box polypeptide 17
    885. 81557 MAGED4 melanoma antigen family D, 4
    886. 10133 OPTN optineurin
    887. 54504 CPVL carboxypeptidase, vitellogenic-like
    888. 64062 C13orf10 chromosome 13 open reading frame 10
    889. 401115 LOC401115 hypothetical gene supported by BC038466;
    BC062790
    890. 6892 TAPBP TAP binding protein (tapasin)
    891. 8087 FXR1 fragile X mental retardation, autosomal homolog 1
    892. 7905 C5orf18 chromosome 5 open reading frame 18
    893. 3916 LAMP1 lysosomal-associated membrane protein 1
    894. 22982 KIAA0934 KIAA0934
    895. 55615 PRR5 proline rich protein 5
    896. 5651 PRSS7 protease, serine, 7 (enterokinase)
    897. 10449 ACAA2 acetyl-Coenzyme A acyltransferase 2 (mitochondrial
    3-oxoacyl-Coenzyme A thiolase)
    898. 8934 RAB7L1 RAB7, member RAS oncogene family-like 1
    899. 10114 HIPK3 homeodomain interacting protein kinase 3
    900. 57560 WDR56 WD repeat domain 56
    901. 51205 ACP6 acid phosphatase 6, lysophosphatidic
    902. 6238 RRBP1 ribosome binding protein 1 homolog 180 kDa (dog)
    903. 151011 SEPT10 septin 10
    904. 22920 KIFAP3 kinesin-associated protein 3
    905. 3958 LGALS3 lectin, galactoside-binding, soluble, 3 (galectin 3)
    906. 84186 ZCCHC7 zinc finger, CCHC domain containing 7
    907. 9452 ITM2A integral membrane protein 2A
    908. 10159 ATP6AP2 ATPase, H+ transporting, lysosomal accessory
    protein 2
    909. 23641 LDOC1 leucine zipper, down-regulated in cancer 1
    910. 967 CD63 CD63 antigen (melanoma 1 antigen)
    911. 2517 FUCA1 fucosidase, alpha-L-1, tissue
    912. 23219 FBXO28 F-box protein 28
    913. 79982 DNAJB14 DnaJ (Hsp40) homolog, subfamily B, member 14
    914. 7328 UBE2H ubiquitin-conjugating enzyme E2H (UBC8 homolog,
    yeast)
    915. 23355 KIAA0804 KIAA0804
    916. 257103 C21orf86 chromosome 21 open reading frame 86
    917. 6307 SC4MOL sterol-C4-methyl oxidase-like
    918. 23376 KIAA0776 KIAA0776
    919. 57700 KIAA1600 KIAA1600
    920. 85461 TANC TPR domain, ankyrin-repeat and coiled-coil-
    containing
    921. 4247 MGAT2 mannosyl (alpha-1,6-)-glycoprotein beta-1,2-N-
    acetylglucosaminyltransferase
    922. 3383 ICAM1 intercellular adhesion molecule 1 (CD54), human
    rhinovirus receptor
    923. 493812 HCG11 HLA complex group 11
    924. 5921 RASA1 RAS p21 protein activator (GTPase activating
    protein) 1
    925. 23563 CHST5 carbohydrate (N-acetylglucosamine 6-O)
    sulfotransferase 5
    926. 51100 SH3GLB1 SH3-domain GRB2-like endophilin B1
    927. 339988 LOC339988 hypothetical protein LOC339988
    928. 79080 MGC2574 hypothetical protein MGC2574
    929. 55761 TTC17 tetratricopeptide repeat domain 17
    930. 144871 LOC144871 hypothetical protein LOC144871
    931. 4194 MDM4 Mdm4, transformed 3T3 cell double minute 4, p53
    binding protein (mouse)
    932. 51030 FAM18B family with sequence similarity 18, member B
    933. 1650 DDOST dolichyl-diphosphooligosaccharide-protein
    glycosyltransferase
    934. 147463 ANKRD29 ankyrin repeat domain 29
    935. 3757 KCNH2 potassium voltage-gated channel, subfamily H (eag-
    related), member 2
    936. 116442 RAB39B RAB39B, member RAS oncogene family
    937. 10972 TMP21 transmembrane trafficking protein
    938. 57798 GATAD1 GATA zinc finger domain containing 1
    939. 1314 COPA coatomer protein complex, subunit alpha
    940. 2581 GALC galactosylceramidase (Krabbe disease)
    941. 91452 ACBD5 acyl-Coenzyme A binding domain containing 5
    942. 8879 SGPL1 sphingosine-1-phosphate lyase 1
    943. 4897 NRCAM neuronal cell adhesion molecule
    944. 23209 MLC1 megalencephalic leukoencephalopathy with
    subcortical cysts 1
    945. 440270 LOC440270 golgin-67
    946. 5034 P4HB procollagen-proline, 2-oxoglutarate 4-dioxygenase
    (proline 4-hydroxylase), beta polypeptide (protein
    disulfide isomerase-associated 1)
    947. 148646 FLJ32096 hypothetical protein FLJ32096
    948. 399917 LOC399917 similar to polymerase
    949. 7096 TLR1 toll-like receptor 1
    950. 80853 KIAA1718 KIAA1718 protein
    951. 378938 MALAT1 metastasis associated lung adenocarcinoma
    transcript 1 (non-coding RNA)
    952. 1266 CNN3 calponin 3, acidic
    953. 58486 LOC58486 transposon-derived Buster1 transposase-like protein
    gene
    954. 1040 CDS1 CDP-diacylglycerol synthase (phosphatidate
    cytidylyltransferase) 1
    955. 9895 KIAA0329 KIAA0329
    956. 1509 CTSD cathepsin D (lysosomal aspartyl protease)
    957. 26115 DKFZP564D166 putative ankyrin-repeat containing protein
    958. 57162 PELI1 pellino homolog 1 (Drosophila)
    959. 57599 WDR48 WD repeat domain 48
    960. 285464 FLJ34443 hypothetical protein FLJ34443
    961. 55857 C20orf19 chromosome 20 open reading frame 19
    962. 339456 LOC339456 hypothetical protein LOC339456
    963. 51569 UFM1 ubiquitin-fold modifier 1
    964. 582 BBS1 Bardet-Biedl syndrome 1
    965. 4637 MYL6 myosin, light polypeptide 6, alkali, smooth muscle
    and non-muscle
    966. 1186 CLCN7 chloride channel 7
    967. 3490 IGFBP7 insulin-like growth factor binding protein 7
    968. 5095 PCCA propionyl Coenzyme A carboxylase, alpha
    polypeptide
    969. 10966 RAB40B RAB40B, member RAS oncogene family
    970. 285362 SUMF1 sulfatase modifying factor 1
    971. 56122 PCDHB14 protocadherin beta 14
    972. 57534 MIB1 mindbomb homolog 1 (Drosophila)
    973. 56951 C5orf15 chromosome 5 open reading frame 15
    974. 113177 C19orf36 chromosome 19 open reading frame 36
    975. 10379 ISGF3G interferon-stimulated transcription factor 3, gamma
    48 kDa
    976. 64224 FLJ22313 hypothetical protein FLJ22313
    977. 65084 FLJ22104 hypothetical protein FLJ22104
    978. 10537 UBD ubiquitin D
    979. 8548 BLZF1 basic leucine zipper nuclear factor 1 (JEM-1)
    980. 284214 LOC284214 hypothetical protein LOC284214
    981. 8334 HIST1H2AC histone 1, H2ac
    982. 80210 FLJ12584 melanoma/melanocyte specific protein KU-MEL-1
    983. 1182 CLCN3 chloride channel 3
    984. 26751 SH3YL1 SH3 domain containing, Ysc84-like 1 (S. cerevisiae)
    985. 114327 EFHC1 EF-hand domain (C-terminal) containing 1
    986. 7351 UCP2 uncoupling protein 2 (mitochondrial, proton carrier)
    987. 10724 MGEA5 meningioma expressed antigen 5 (hyaluronidase)
    988. 9652 KIAA0372 KIAA0372
    989. 200958 MUC20 mucin 20
    990. 161527 LOC161527 hypothetical protein LOC161527
    991. 10314 LANCL1 LanC lantibiotic synthetase component C-like 1
    (bacterial)
    992. 2923 PDIA3 protein disulfide isomerase family A, member 3
    993. 84247 LDOC1L leucine zipper, down-regulated in cancer 1-like
    994. 3006 HIST1H1C histone1, H1c
    995. 9562 MINPP1 multiple inositol polyphosphate histidine
    phosphatase, 1
    996. 115024 MGC20781 hypothetical protein MGC20781
    997. 65982 FLJ12895 hypothetical protein FLJ12895
    998. 5268 SERPINB5 serine (or cysteine) proteinase inhibitor, clade B
    (ovalbumin), member 5
    999. 94240 EPSTI1 epithelial stromal interaction 1 (breast)
    1000. 2621 GAS6 growth arrest-specific 6
    1001. 401024 FLJ44048 FLJ44048 protein
    1002. 57142 RTN4 reticulon 4
    1003. 50854 C6orf48 chromosome 6 open reading frame 48
    1004. 317649 EIF4E3 eukaryotic translation initiation factor 4E member 3
    1005. 4179 MCP membrane cofactor protein (CD46, trophoblast-
    lymphocyte cross-reactive antigen)
    1006. 54884 RetSat all-trans-13,14-dihydroretinol saturase
    1007. 10154 PLXNC1 plexin C1
    1008. 2630 GBAP glucosidase, beta; acid, pseudogene
    1009. 7077 TIMP2 tissue inhibitor of metalloproteinase 2
    1010. 23741 CRI1 CREBBP/EP300 inhibitor 1
    1011. 949 SCARB1 scavenger receptor class B, member 1
    1012. 1519 CTSO cathepsin O
    1013. 51136 LOC51136 PTD016 protein
    1014. 3428 IFI16 interferon, gamma-inducible protein 16
    1015. 9516 LITAF lipopolysaccharide-induced TNF factor
    1016. 3123 HLA-DRB1 major histocompatibility complex, class II, DR beta 1
    1017. 1389 CREBL2 cAMP responsive element binding protein-like 2
    1018. 5027 P2RX7 purinergic receptor P2X, ligand-gated ion channel, 7
    1019. 6782 STCH stress 70 protein chaperone, microsome-associated,
    60 kDa
    1020. 5645 PRSS2 protease, serine, 2 (trypsin 2)
    1021. 84282 RNF135 ring finger protein 135
    1022. 9852 EPM2AIP1 EPM2A (laforin) interacting protein 1
    1023. 84333 PCGF5 polycomb group ring finger 5
    1024. 23475 QPRT quinolinate phosphoribosyltransferase (nicotinate-
    nucleotide pyrophosphorylase (carboxylating))
    1025. 11142 PKIG protein kinase (cAMP-dependent, catalytic) inhibitor
    gamma
    1026. 54832 VPS13C vacuolar protein sorting 13C (yeast)
    1027. 1486 CTBS chitobiase, di-N-acetyl-
    1028. 4601 MXI1 MAX interactor 1
    1029. 1365 CLDN3 claudin 3
    1030. 81622 UNC93B1 unc-93 homolog B1 (C. elegans)
    1031. 54664 FLJ11273 hypothetical protein FLJ11273
    1032. 9993 DGCR2 DiGeorge syndrome critical region gene 2
    1033. 57179 KIAA1191 KIAA1191 protein
    1034. 55958 KLHL9 kelch-like 9 (Drosophila)
    1035. 81671 TMEM49 transmembrane protein 49
    1036. 9666 DZIP3 zinc finger DAZ interacting protein 3
    1037. 10509 SEMA4B sema domain, immunoglobulin domain (Ig),
    transmembrane domain (TM) and short cytoplasmic
    domain, (semaphorin) 4B
    1038. 3782 KCNN3 potassium intermediate/small conductance calcium-
    activated channel, subfamily N, member 3
    1039. 4644 MYO5A myosin VA (heavy polypeptide 12, myoxin)
    1040. 55179 FAIM Fas apoptotic inhibitory molecule
    1041. 9687 GREB1 GREB1 protein
    1042. 25861 DFNB31 deafness, autosomal recessive 31
    1043. 9197 SLC33A1 solute carrier family 33 (acetyl-CoA transporter),
    member 1
    1044. 10549 PRDX4 peroxiredoxin 4
    1045. 27090 ST6GALNAC4 ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-
    1,3)-N-acetylgalactosaminide alpha-2,6-
    sialyltransferase 4
    1046. 3988 LIPA lipase A, lysosomal acid, cholesterol esterase
    (Wolman disease)
    1047. 10577 NPC2 Niemann-Pick disease, type C2
    1048. 441951 HSUP1 similar to RPE-spondin
    1049. 26275 HIBCH 3-hydroxyisobutyryl-Coenzyme A hydrolase
    1050. 401397 LOC401397 hypothetical LOC401397
    1051. 81555 YIPF5 Yip1 domain family, member 5
    1052. 19 ABCA1 ATP-binding cassette, sub-family A (ABC1), member 1
    1053. 2896 GRN granulin
    1054. 1312 COMT catechol-O-methyltransferase
    1055. 127018 LYPLAL1 lysophospholipase-like 1
    1056. 5911 RAP2A RAP2A, member of RAS oncogene family
    1057. 3017 HIST1H2BD histone 1, H2bd
    1058. 9139 CBFA2T2 core-binding factor, runt domain, alpha subunit 2;
    translocated to, 2
    1059. 50848 F11R F11 receptor
    1060. 3728 JUP junction plakoglobin
    1061. 8615 VDP vesicle docking protein p115
    1062. 79090 MGC2650 hypothetical protein MGC2650
    1063. 51303 FKBP11 FK506 binding protein 11, 19 kDa
    1064. 64747 MFSD1 major facilitator superfamily domain containing 1
    1065. 23471 TRAM1 translocation associated membrane protein 1
    1066. 1832 DSP desmoplakin
    1067. 125144 MGC40157 hypothetical protein MGC40157
    1068. 10150 MBNL2 muscleblind-like 2 (Drosophila)
    1069. 3082 HGF hepatocyte growth factor (hepapoietin A; scatter
    factor)
    1070. 7750 ZNF198 zinc finger protein 198
    1071. 2908 NR3C1 nuclear receptor subfamily 3, group C, member 1
    (glucocorticoid receptor)
    1072. 25758 G2 G2 protein
    1073. 10653 SPINT2 serine protease inhibitor, Kunitz type, 2
    1074. 116151 C20orf108 chromosome 20 open reading frame 108
    1075. 8933 CXX1 CAAX box 1
    1076. 475 ATOX1 ATX1 antioxidant protein 1 homolog (yeast)
    1077. 23406 COTL1 coactosin-like 1 (Dictyostelium)
    1078. 57561 ARRDC3 arrestin domain containing 3
    1079. 55205 ZNF532 zinc finger protein 532
    1080. 25796 PGLS 6-phosphogluconolactonase
    1081. 283846 DKFZp547E087 PI-3-kinase-related kinase SMG-1-like
    1082. 57185 DJ462O23.2 hypothetical protein dJ462O23.2
    1083. 54431 DNAJC10 DnaJ (Hsp40) homolog, subfamily C, member 10
    1084. 5800 PTPRO protein tyrosine phosphatase, receptor type, O
    1085. 1465 CSRP1 cysteine and glycine-rich protein 1
    1086. 950 SCARB2 scavenger receptor class B, member 2
    1087. 51019 CGI-116 CGI-116 protein
    1088. 5476 PPGB protective protein for beta-galactosidase
    (galactosialidosis)
    1089. 54145 H2BFS H2B histone family, member S
    1090. 65981 C1QDC1 C1q domain containing 1
    1091. 81502 HM13 histocompatibility (minor) 13
    1092. 3572 IL6ST interleukin 6 signal transducer (gp130, oncostatin M
    receptor)
    1093. 1299 COL9A3 collagen, type IX, alpha 3
    1094. 1386 ATF2 activating transcription factor 2
    1095. 4134 MAP4 microtubule-associated protein 4
    1096. 3981 LIG4 ligase IV, DNA, ATP-dependent
    1097. 57714 KIAA1618 KIAA1618
    1098. 80315 CPEB4 cytoplasmic polyadenylation element binding protein 4
    1099. 107 ADCY1 adenylate cyclase 1 (brain)
    1100. 8804 CREG1 cellular repressor of E1A-stimulated genes 1
    1101. 84181 CHD6 chromodomain helicase DNA binding protein 6
    1102. 22871 NLGN1 neuroligin 1
    1103. 659 BMPR2 bone morphogenetic protein receptor, type II
    (serine/threonine kinase)
    1104. 79158 MGC4170 MGC4170 protein
    1105. 112399 EGLN3 egl nine homolog 3 (C. elegans)
    1106. 10550 ARL6IP5 ADP-ribosylation-like factor 6 interacting protein 5
    1107. 55573 H41 hypothetical protein H41
    1108. 51706 NQO3A2 NAD(P)H:quinone oxidoreductase type 3,
    polypeptide A2
    1109. 79738 FLJ23560 hypothetical protein FLJ23560
    1110. 6672 SP100 nuclear antigen Sp100
    1111. 145173 B3GTL beta 3-glycosyltransferase-like
    1112. 3275 HRMT1L1 HMT1 hnRNP methyltransferase-like 1 (S. cerevisiae)
    1113. 54059 C21orf57 chromosome 21 open reading frame 57
    1114. 571 BACH1 BTB and CNC homology 1, basic leucine zipper
    transcription factor 1
    1115. 6990 TCTE1L t-complex-associated-testis-expressed 1-like
    1116. 9341 VAMP3 vesicle-associated membrane protein 3 (cellubrevin)
    1117. 2180 ACSL1 acyl-CoA synthetase long-chain family member 1
    1118. 2799 GNS glucosamine (N-acetyl)-6-sulfatase (Sanfilippo
    disease IIID)
    1119. 9236 CCPG1 cell cycle progression 1
    1120. 51111 SUV420H1 suppressor of variegation 4-20 homolog 1
    (Drosophila)
    1121. 598 BCL2L1 BCL2-like 1
    1122. 57674 C17orf27 chromosome 17 open reading frame 27
    1123. 1488 CTBP2 C-terminal binding protein 2
    1124. 80267 C1orf22 chromosome 1 open reading frame 22
    1125. 90701 SEC11L3 SEC11-like 3 (S. cerevisiae)
    1126. 84218 TBC1D3 TBC1 domain family, member 3
    1127. 7844 RNF103 ring finger protein 103
    1128. 8440 NCK2 NCK adaptor protein 2
    1129. 25934 NIPSNAP3A nipsnap homolog 3A (C. elegans)
    1130. 3897 L1CAM L1 cell adhesion molecule
    1131. 114915 TIGA1 TIGA1
    1132. 754 PTTG1IP pituitary tumor-transforming 1 interacting protein
    1133. 10525 HYOU1 hypoxia up-regulated 1
    1134. 966 CD59 CD59 antigen p18-20 (antigen identified by
    monoclonal antibodies 16.3A5, EJ16, EJ30, EL32
    and G344)
    1135. 25976 TIPARP TCDD-inducible poly(ADP-ribose) polymerase
    1136. 3714 JAG2 jagged 2
    1137. 8780 RIOK3 RIO kinase 3 (yeast)
    1138. 55827 IQWD1 IQ motif and WD repeats 1
    1139. 55830 GLT8D1 glycosyltransferase 8 domain containing 1
    1140. 4779 NFE2L1 nuclear factor (erythroid-derived 2)-like 1
    1141. 7286 TUFT1 tuftelin 1
    1142. 1028 CDKN1C cyclin-dependent kinase inhibitor 1C (p57, Kip2)
    1143. 60492 MDS025 hypothetical protein MDS025
    1144. 27319 BHLHB5 basic helix-loop-helix domain containing, class B, 5
    1145. 1958 EGR1 early growth response 1
    1146. 89796 NAV1 neuron navigator 1
    1147. 9240 PNMA1 paraneoplastic antigen MA1
    1148. 6773 STAT2 signal transducer and activator of transcription 2,
    113 kDa
    1149. 7494 XBP1 X-box binding protein 1
    1150. 11057 ABHD2 abhydrolase domain containing 2
    1151. 9451 EIF2AK3 eukaryotic translation initiation factor 2-alpha kinase 3
    1152. 8878 SQSTM1 sequestosome 1
    1153. 302 ANXA2 annexin A2
    1154. 2590 GALNT2 UDP-N-acetyl-alpha-D-galactosamine:polypeptide
    N-acetylgalactosaminyltransferase 2 (GalNAc-T2)
    1155. 1200 TPP1 tripeptidyl peptidase I
    1156. 5973 RENBP renin binding protein
    1157. 7259 TSPYL1 TSPY-like 1
    1158. 112770 C1orf85 chromosome 1 open reading frame 85
    1159. 93953 ACRC acidic repeat containing
    1160. 90634 CG018 hypothetical gene CG018
    1161. 1030 CDKN2B cyclin-dependent kinase inhibitor 2B (p15, inhibits
    CDK4)
    1162. 158158 RASEF RAS and EF hand domain containing
    1163. 2824 GPM6B glycoprotein M6B
    1164. 9706 ULK2 unc-51-like kinase 2 (C. elegans)
    1165. 92370 ACPL2 acid phosphatase-like 2
    1166. 1203 CLN5 ceroid-lipofuscinosis, neuronal 5
    1167. 8337 HIST2H2AA histone 2, H2aa
    1168. 3998 LMAN1 lectin, mannose-binding, 1
    1169. 56675 NRIP3 nuclear receptor interacting protein 3
    1170. 4864 NPC1 Niemann-Pick disease, type C1
    1171. 3358 HTR2C 5-hydroxytryptamine (serotonin) receptor 2C
    1172. 304 ANXA2P2 annexin A2 pseudogene 2
    1173. 81790 RNF170 ring finger protein 170
    1174. 2537 G1P3 interferon, alpha-inducible protein (clone IFI-6-16)
    1175. 55251 C20orf36 chromosome 20 open reading frame 36
    1176. 27344 PCSK1N proprotein convertase subtilisin/kexin type 1 inhibitor
    1177. 10057 ABCC5 ATP-binding cassette, sub-family C (CFTR/MRP),
    member 5
    1178. 81031 SLC2A10 solute carrier family 2 (facilitated glucose
    transporter), member 10
    1179. 467 ATF3 activating transcription factor 3
    1180. 94103 ORMDL3 ORM1-like 3 (S. cerevisiae)
    1181. 375593 TRIM50B tripartite motif-containing 50B
    1182. 23015 GM88 88-kDa golgi protein
    1183. 55818 JMJD1A jumonji domain containing 1A
    1184. 5274 SERPINI1 serine (or cysteine) proteinase inhibitor, clade I
    (neuroserpin), member 1
    1185. 23336 DMN desmuslin
    1186. 255631 COL24A1 collagen, type XXIV, alpha 1
    1187. 3995 FADS3 fatty acid desaturase 3
    1188. 5797 PTPRM protein tyrosine phosphatase, receptor type, M
    1189. 55876 GSDML gasdermin-like
    1190. 999 CDH1 cadherin 1, type 1, E-cadherin (epithelial)
    1191. 84897 TBRG1 transforming growth factor beta regulator 1
    1192. 51363 GALNAC4S-6ST B cell RAG associated protein
    1193. 9961 MVP major vault protein
    1194. 2982 GUCY1A3 guanylate cyclase 1, soluble, alpha 3
    1195. 706 BZRP benzodiazapine receptor (peripheral)
    1196. 144203 OVOS2 ovostatin 2
    1197. 8516 ITGA8 integrin, alpha 8
    1198. 2037 EPB41L2 erythrocyte membrane protein band 4.1-like 2
    1199. 1524 CX3CR1 chemokine (C—X3—C motif) receptor 1
    1200. 222166 Ells1 hypothetical protein Ells1
    1201. 339803 LOC339803 hypothetical protein LOC339803
    1202. 5360 PLTP phospholipid transfer protein
    1203. 1612 DAPK1 death-associated protein kinase 1
    1204. 90161 HS6ST2 heparan sulfate 6-O-sulfotransferase 2
    1205. 115701 ALPK2 alpha-kinase 2
    1206. 50640 IPLA2(GAMMA) intracellular membrane-associated calcium-
    independent phospholipase A2 gamma
    1207. 8473 OGT O-linked N-acetylglucosamine (GlcNAc) transferase
    (UDP-N-acetylglucosamine:polypeptide-N-
    acetylglucosaminyl transferase)
    1208. 252839 TMEM9 transmembrane protein 9
    1209. 150759 LOC150759 hypothetical protein LOC150759
    1210. 401152 LOC401152 HCV F-transactivated protein 1
    1211. 64065 PERP PERP, TP53 apoptosis effector
    1212. 114793 FMNL2 formin-like 2
    1213. 477 ATP1A2 ATPase, Na+/K+ transporting, alpha 2 (+)
    polypeptide
    1214. 59338 PLEKHA1 pleckstrin homology domain containing, family A
    (phosphoinositide binding specific) member 1
    1215. 3727 JUND jun D proto-oncogene
    1216. 85236 HIST1H2BK histone 1, H2bk
    1217. 6513 SLC2A1 solute carrier family 2 (facilitated glucose
    transporter), member 1
    1218. 155038 GIMAP8 GTPase, IMAP family member 8
    1219. 3055 HCK hemopoietic cell kinase
    1220. 6542 SLC7A2 solute carrier family 7 (cationic amino acid
    transporter, y+ system), member 2
    1221. 8996 NOL3 nucleolar protein 3 (apoptosis repressor with CARD
    domain)
    1222. 9728 KIAA0256 KIAA0256 gene product
    1223. 51237 PACAP proapoptotic caspase adaptor protein
    1224. 8987 GENX-3414 genethonin 1
    1225. 132720 FLJ39370 hypothetical protein FLJ39370
    1226. 1601 DAB2 disabled homolog 2, mitogen-responsive
    phosphoprotein (Drosophila)
    1227. 54741 LEPROT leptin receptor overlapping transcript
    1228. 81631 MAP1LC3B microtubule-associated protein 1 light chain 3 beta
    1229. 9473 C1orf38 chromosome 1 open reading frame 38
    1230. 94241 TP53INP1 tumor protein p53 inducible nuclear protein 1
    1231. 5816 PVALB parvalbumin
    1232. 115294 LOC115294 similar to hypothetical protein FLJ10883
    1233. 23461 ABCA5 ATP-binding cassette, sub-family A (ABC1), member 5
    1234. 10370 CITED2 Cbp/p300-interacting transactivator, with Glu/Asp-
    rich carboxy-terminal domain, 2
    1235. 9604 RNF14 ring finger protein 14
    1236. 387263 C6orf120 chromosome 6 open reading frame 120
    1237. 9120 SLC16A6 solute carrier family 16 (monocarboxylic acid
    transporters), member 6
    1238. 3915 LAMC1 laminin, gamma 1 (formerly LAMB2)
    1239. 23092 ARHGAP26 Rho GTPase activating protein 26
    1240. 64778 FNDC3B fibronectin type III domain containing 3B
    1241. 10140 TOB1 transducer of ERBB2, 1
    1242. 23208 SYT11 synaptotagmin XI
    1243. 57730 KIAA1641 KIAA1641
    1244. 120196 MGC34830 hypothetical protein MGC34830
    1245. 7832 BTG2 BTG family, member 2
    1246. 23259 DDHD2 DDHD domain containing 2
    1247. 84981 MGC14376 hypothetical protein MGC14376
    1248. 6448 SGSH N-sulfoglucosamine sulfohydrolase (sulfamidase)
    1249. 9910 RABGAP1L RAB GTPase activating protein 1-like
    1250. 1611 DAP death-associated protein
    1251. 126823 KARCA1 kelch/ankyrin repeat containing cyclin A1 interacting
    protein
    1252. 388403 YPEL2 yippee-like 2 (Drosophila)
    1253. 6720 SREBF1 sterol regulatory element binding transcription factor 1
    1254. 58476 TP53INP2 tumor protein p53 inducible nuclear protein 2
    1255. 8605 PLA2G4C phospholipase A2, group IVC (cytosolic, calcium-
    independent)
    1256. 3983 ABLIM1 actin binding LIM protein 1
    1257. 4189 DNAJB9 DnaJ (Hsp40) homolog, subfamily B, member 9
    1258. 1604 DAF decay accelerating factor for complement (CD55,
    Cromer blood group system)
    1259. 29994 BAZ2B bromodomain adjacent to zinc finger domain, 2B
    1260. 10156 RASA4 RAS p21 protein activator 4
    1261. 9123 SLC16A3 solute carrier family 16 (monocarboxylic acid
    transporters), member 3
    1262. 7846 TUBA3 tubulin, alpha 3
    1263. 3956 LGALS1 lectin, galactoside-binding, soluble, 1 (galectin 1)
    1264. 1647 GADD45A growth arrest and DNA-damage-inducible, alpha
    1265. 6609 SMPD1 sphingomyelin phosphodiesterase 1, acid lysosomal
    (acid sphingomyelinase)
    1266. 56904 SH3GLB2 SH3-domain GRB2-like endophilin B2
    1267. 440081 DDX12 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 12
    (CHL1-like helicase homolog, S. cerevisiae)
    1268. 5163 PDK1 pyruvate dehydrogenase kinase, isoenzyme 1
    1269. 25840 DKFZP586A0522 DKFZP586A0522 protein
    1270. 51566 ARMCX3 armadillo repeat containing, X-linked 3
    1271. 9388 LIPG lipase, endothelial
    1272. 27250 PDCD4 programmed cell death 4 (neoplastic transformation
    inhibitor)
    1273. 6302 SAS sarcoma amplified sequence
    1274. 83937 RASSF4 Ras association (RalGDS/AF-6) domain family 4
    1275. 388677 NOTCH2NL Notch homolog 2 (Drosophila) N-terminal like
    1276. 23646 PLD3 phospholipase D family, member 3
    1277. 23643 LY96 lymphocyte antigen 96
    1278. 9855 FARP2 FERM, RhoGEF and pleckstrin domain protein 2
    1279. 65018 PINK1 PTEN induced putative kinase 1
    1280. 57035 C1orf63 chromosome 1 open reading frame 63
    1281. 85352 KIAA1644 KIAA1644 protein
    1282. 283131 TncRNA trophoblast-derived noncoding RNA
    1283. 143888 KDELC2 KDEL (Lys-Asp-Glu-Leu) containing 2
    1284. 56204 FLJ10980 hypothetical protein FLJ10980
    1285. 23446 CDW92 CDW92 antigen
    1286. 23766 GABARAPL3 GABA(A) receptors associated protein like 3
    1287. 1508 CTSB cathepsin B
    1288. 4094 MAF v-maf musculoaponeurotic fibrosarcoma oncogene
    homolog (avian)
    1289. 22932 POMZP3 POM (POM121 homolog, rat) and ZP3 fusion
    1290. 56243 KIAA1217 KIAA1217
    1291. 1663 DDX11 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11
    (CHL1-like helicase homolog, S. cerevisiae)
    1292. 1414 CRYBB1 crystallin, beta B1
    1293. 154091 SLC2A12 solute carrier family 2 (facilitated glucose
    transporter), member 12
    1294. 4121 MAN1A1 mannosidase, alpha, class 1A, member 1
    1295. 11178 LZTS1 leucine zipper, putative tumor suppressor 1
    1296. 10628 TXNIP thioredoxin interacting protein
    1297. 83719 YPEL3 yippee-like 3 (Drosophila)
    1298. 9863 MAGI2 membrane associated guanylate kinase, WW and
    PDZ domain containing 2
    1299. 5660 PSAP prosaposin (variant Gaucher disease and variant
    metachromatic leukodystrophy)
    1300. 145788 FLJ27352 hypothetical LOC145788
    1301. 84513 HTPAP HTPAP protein
    1302. 57612 KIAA1466 KIAA1466 gene
    1303. 57515 TDE2 tumor differentially expressed 2
    1304. 29005 PRO1073 PRO1073 protein
    1305. 51646 YPEL5 yippee-like 5 (Drosophila)
    1306. 5269 SERPINB6 serine (or cysteine) proteinase inhibitor, clade B
    (ovalbumin), member 6
    1307. 30061 SLC40A1 solute carrier family 40 (iron-regulated transporter),
    member 1
    1308. 81030 ZBP1 Z-DNA binding protein 1
    1309. 347733 RP11-506K6.1 tubulin, beta polypeptide paralog
    1310. 390 RND3 Rho family GTPase 3
    1311. 10765 JARID1B Jumonji, AT rich interactive domain 1B (RBP2-like)
    1312. 9783 RIMS3 regulating synaptic membrane exocytosis 3
    1313. 27122 DKK3 dickkopf homolog 3 (Xenopus laevis)
    1314. 151556 GPR155 G protein-coupled receptor 155
    1315. 8365 HIST1H4H histone 1, H4h
    1316. 6480 ST6GAL1 ST6 beta-galactosamide alpha-2,6-sialyltranferase 1
    1317. 6591 SNAI2 snail homolog 2 (Drosophila)
    1318. 54800 DRE1 DRE1 protein
    1319. 3669 ISG20 interferon stimulated exonuclease gene 20 kDa
    1320. 23710 GABARAPL1 GABA(A) receptor-associated protein like 1
    1321. 400172 LOC400172 similar to KIAA1641 protein; melanoma-associated
    antigen; CLL-associated antigen KW-1
    1322. 153222 LOC153222 adult retina protein
    1323. 54981 C9orf95 chromosome 9 open reading frame 95
    1324. 5641 LGMN legumain
    1325. 257019 FRMD3 FERM domain containing 3
    1326. 8357 HIST1H3H histone 1, H3h
    1327. 55281 FLJ11000 hypothetical protein FLJ11000
    1328. 4050 LTB lymphotoxin beta (TNF superfamily, member 3)
    1329. 203 AK1 adenylate kinase 1
    1330. 5920 RARRES3 retinoic acid receptor responder (tazarotene
    induced) 3
    1331. 284801 LOC284801 hypothetical protein LOC284801
    1332. 150271 LOC150271 hypothetical protein LOC150271
  • TABLE II
    ENTREZ
    GENE ID GENE SYMBOL GENE DESCRIPTION
     1. 6348 CCL3 chemokine (C-C motif) ligand 3
     2. 55388 MCM10 MCM10 minichromosome maintenance deficient 10
    (S. cerevisiae)
     3. 7117 TMSL3 thymosin-like 3
     4. 1017 CDK2 cyclin-dependent kinase 2
     5. 79019 C22orf18 chromosome 22 open reading frame 18
     6. 6241 RRM2 ribonucleotide reductase M2 polypeptide
     7. 4605 MYBL2 v-myb myeloblastosis viral oncogene homolog
    (avian)-like 2
     8. 894 CCND2 cyclin D2
     9. 57405 SPBC25 spindle pole body component 25 homolog (S.
    cerevisiae)
     10. 136909 LOC146909 hypothetical protein LOC146909
     11. 150271 LOC150271 hypothetical protein LOC150271
     12. 203 AK1 adenylate kinase 1
     13. 4050 LTB lymphotoxin beta (THF superfamily, member 3)
     14. 257019 FRMD3 FERM domain containing 3
     15. 8357 HIST1H3H histone 1, H3h
     16. 23710 GABARAPL1 GABA(A) receptor-associated protein like 1
     17. 4171 MCM2 MCM2 minichromosome maintenance deficient 2,
    mitotin (S. cerevisiae)
     18. 4176 MCM7 MCM7 minichromosome maintenance deficient 7
    (S. cerevisiae)
     19. 29089 UBE2T ubiquitin-conjugating enzyme E2T (putative)
     20. 890 CCNA2 cyclin A2
     21. 51514 DTL denticleless homolog (Drosophila)
     22. 440279 UNC13C unc-13 homolog C (C. elegans)
     23. 11130 ZWINT ZW10 interactor
     24. 9768 KIAA0101 KIAA0101
     25. 27338 UBE2S ubiquitin-conjugating enzyme E2S
     26. 1846 DUSP4 dual specificity phosphatase 4
     27. 9833 MELK maternal embryonic leucine zipper kinase
     28. 387103 C6orf173 chromosome 6 open reading frame 173
     29. 137392 LOC137392 similar to CG6405 gene product
     30. 7374 UNG uracil-DNA glycosylase
     31. 4915 NTRK2 neurotrophic tyrosine kinase, receptor, type 2
     32. 990 CDC6 CDC6 cell division cycle 6 homolog (S. cerevisiae)
     33. 55165 C10orf3 chromosome 10 open reading frame 3
     34. 4001 LMNB1 lamin B1
     35. 51659 Pfs2 DNA replication complex GINS protein PSF2
     36. 11065 UBEC2 ubiquitin-conjugating enzyme E2C
     37. 4174 MCM5 MCM5 minichromosome maintenance defieicnt 5,
    cell division cycle 46 (S. cerevisiae)
     38. 113130 CDCA5 cell division cycle associated 5
     39. 9535 GMFG glia maturation factor, gamma
     40. 195828 ZNF367 zinc finger protein 367
     41. 55355 DKFZp762E1312 hypothetical protein DKFZp762E1312
     42. 9928 KIF14 kinesin family member 14
     43. 83879 CDCA7 cell division cycle associated 7
     44. 701 BUB1B BUB1 budding uninhibited by benzimidazoles 1
    homolog beta (yeats)
     45. 200734 SPRED2 sprouty-related, EVH1 domain containing 2
     46. 991 CDC20 CDC20 cell division cycle 20 homolog (S.
    cerevisiae)
     47. 22974 TPX2 TPX2, microtubule-associated protein homolog
    (Xenopus laevis)
     48. 3832 KIF11 kinesin family member 11
     49. 4288 MKI67 antigen identified by monoclonal antibody Ki-67
     50. 983 CDC2 cell division cycle 2, G1 to S and G2 to M
     51. 28231 SLCO4A1 solute carrier organic anion transporter family,
    member 4A1
     52. 79801 SHCBP1 SHC SH2-domain binding protein 1
     53. 7804 LRP8 low density lipoprotein receptor-related protein 8,
    apolipoprotein e receptor
     54. 7298 TYMS thymidine kinase 1, soluble
     55. 7083 TK1 thymidine kinase 1, soluble
     56. 26147 PHF19 PHD finger protein 19
     57. 55839 BM039 uncharacterized bone marrow protein BM039
     58. 9232 PTTG1 pituitary tumor-transforming 1
     59. 10592 SMC2L1 SMC2 strutural maintenance of chromosomes 2-
    like 1 (yeast)
     60. 3398 ID2 inhibitor of DNA binding 2, dominant negative helix-
    loop-helix protein
     61. 4085 MAD2L1 MAD2 mitotic arrest deficient-like 1 (yeast)
     62. 1063 CENPF centromere protein F, 350/400ka (mitosin)
     63. 3418 IDH2 isocitrate dehydrogenase 2 (NADP√), mitochondrial
     64. 1163 SKD1B CDC28 protein kinase regulatory subunit 1B
     65. 55215 FLJ10719 hypothetical protein FLJ10719
     66. 29127 RACGAP1 Rac GTPase activating protein 1
     67. 7153 TOP2A topoisomerase (DNA) II alpha 170 kDa
     68. 122769 PPIL5 peptidylprolyl isomerase (cyclophilin)-like 5
     69. 79682 MLF1IP MLF1 interacting protein
     70. 6790 STK6 serine/threonine kinase 6
     71. 3925 STMN1 stathmin 1/oncoprotein 18
     72. 11004 KIF2C kinesin family member 2C
     73. 10276 NET1 neuroepithelial cell transforming gene 1
     74. 3015 H2AFZ H2A histone family, member Z
     75. 891 CCNB1 cyclin B1
     76. 389835 FAAM72A family with sequence similarity 72, member A
     77. 5111 OCNA proliferating cell nuclear antigen
     78. 9837 PSF1 DNA replication complex GINS protein PSF1
     79. 3148 HMGB2 high-mobility group box 2
     80. 7112 TMPO thymopoietin
     81. 63901 FLJ22794 FLJ22794 protein
     82. 51203 NUSAP1 nucleolar and spindle associated protein 1
     83. 29128 UHRF1 ubiquitin-like, containing PHD and RING finger
    domains, 1
     84. 79075 DCC1 defective in sister chromatid cohesion homolog 1 (S.
    cerevisiae)
     85. 9319 TRIP13 thyroid hormone receptor interactor 13
     86. 1033 CDKN3 cyclin-dependent kinase inhibitor 3 (CDK2-
    associated dual specificity phosphatase)
     87. 10189 THOC4 THO complex 4
     88. 9133 CCNB2 cyclin B2
     89. 55010 FLJ20641 hypothetical protein FLJ20641
     90. 83540 CDCA1 cell division cycle associated 1
     91. 1870 E2F2 E2F transcription factor 2
     92. 962 CD48 CD48 antigen (B-cell membrane protein)
     93. 55789 DEPDC1B DEP domain containing 1B
     94. 170954 KIAA1949 KIAA1949
     95. 332 BRIC5 baculoviral IAP repeat-containing 5 (survivin)
     96. 445815 PLAM2-AKAP2 PLAM2-AKAP2 protein
     97. 865 CBFB core-binding factor, beta subunit
     98. 7913 DEK DEK oncogene (DNA binding)
     99. 5983 RFC3 replication factor C (activator 1) 3, 38 kDa
    100. 84515 MCM8 MCM8 minichromosome maintenance deficient 8
    (S. cerevisiae)
    101. 51053 GMNN geminin, DNA replicator inhibitor
    102. 1111 CHEK1 CHK1 checkpoint homolog (S. pombe)
    103. 7443 VRK1 vaccinia related kinase 1
    104. 10376 K-ALPHA-1 tubulin, alpha, ubiquitous
    105. 3014 H2AFX H2A histone family, member X
    106. 9055 PRC1 protein regulator of cytokinesis 1
    107. 2237 FEN1 flap structure-specific endonuclease 1
    108. 81563 C1orf21 chromosome 1 open reading frame 21
    109. 51192 CKLF chemokine-like factor
    110. 1062 CENPA centromere protein E, 312 kDa
    111. 11339 OIP5 Opa interacting protein 5
    112. 10615 SPAG5 sperm associated antigen 5
    113. 55646 LYAR hypothetical protein FLJ20425
    114. 55706 TMEM48 transmembrane protein 48
    115. 1058 CENPA centromere protein A, 17 kDa
    116. 3070 HELLS helicase, lymphoid-specific
    117. 4173 MCM4 MCM4 minichromosome maintenance deficient 4
    (S. cerevisiae)
    118. 23421 ITGB3BP integrin beta 3 binding protein (beta3-endonexin)
    119. 9530 BAG4 BCL2-associated anthanogene 4
    120. 801 CALM1 calmodulin 1 (phosphorylase kinase, delta)
    121. 54069 C21irf45 chromosome 21 open reading frame 45
    122. 283991 MGC29814 hypothetical protein MGC29814
    123. 63979 FIGNL1 fidgetin-like 1
    124. 64105 FKSG14 leucine zipper protein FKSG14
    125. 4172 MCM3 MCM3 minichromosome maintenance deficient 3
    (S. cerevisiae)
    126. 24137 KIF4A kinesin family member 4A
    127. 7398 USP1 ubiquitin specific protease 1
    128. 84930 MASTL microtubule associated serine/threonine kinase-like
    129. 51512 GTSE1 G-2 and S-phase expressed 1
    130. 4678 NASP nuclear autoantigenic sperm protein (histone-
    binding)
    131. 699 BUB1 BUB1 budding uninhibited by benzimidazoles 1
    homolog (yeast)
    132. 1719 DHFR dihydrofolate reductase
    133. 494143 LOC494143 similar to RIKEN cDNA 2510006C20 gene
    134. 55055 FLJ10036 Zwilch
    135. 672 BRCA1 breast cancer 1, early onset
    136. 64946 CENPH centromere protein H
    137. 83461 CDCA3 cell division cycle associated 3
    138. 7465 WEE1 WEE1 homolog (S. pombe)
    139. 5984 RFC4 replication factor C (activator 1) 4, 47 kDa
    140. 64581 CLEC7A C-type lectin domain family 7, member A
    141. 1230 CCR1 chemokine (C-C motif) receptor 1
    142. 4175 MCM6 MCM6 minichromosome maintenance deficient 6
    (MIS5 homolog, S. pombe) (S. cerevisiae)
    143. 55502 HES6 hairy and enhancer of split 6 (Drosophila)
    144. 64151 HCAP-G chromosome condensation protein G
    145. 11151 CORO1A coronin, actin binding protein, 1A
    146. 203068 TUBB tubulin, beta polypeptide
    147. 10926 ASK activator of S phase kinase
    148. 11073 TOPBP1 topoisomerase (DNA) II binding protein 1
    149. 90417 C15orf23 chromosome 15 open reading frame 23
    150. 9493 KIF23 kinesin family member 23
    151. 387882 LOC387882 hypothetical protein
    152. 23234 DNAJC9 DnaJ (Hsp40) homolog, subfamily C, member 9
    153. 2146 EZH2 enhancer of zeste homolog 2 (Drosophila)
    154. 6627 SNRPA1 small nuclear ribonucleoprotein polypeptide A′
    155. 5982 RFC2 replication factor C (activator 1) 2, 40 kDa
    156. 51155 HN1 hematological and neurological expressed 1
    157. 10635 RAD51AP1 RAD51 associated protein 1
    158. 91057 NY-REN-41 NY-REN-41 antigen
    159. 11168 PSIP1 PC4 and SFRS1 interacting protein 1
    160. 10403 KNTC2 kinetochore associated 2
    161. 4751 NEK2 NIMA (never in mitosis gene a)-related kinase 2
    162. 29028 ATAD2 ATPase family, AAA domain containing 2
    163. 26271 PBXO5 F-box protein 5
    164. 54892 LUZP5 leucine zipper protein 5
    165. 79723 SUV39H2 suppressor of variegation 3-9 homolog 2
    (Drosophila)
    166. 23590 TPRT trans-prenyltrasferase
    167. 2288 FKBP4 FK506 binding protein 4, 59 kDa
    168. 23165 NUP205 nucleoporin 205 kDa
    169. 6240 RRM1 ribonucleotide reductase M1 polypeptide
    170. 81539 SLC38A1 solute carrier family 38, member 1
    171. 1894 ECT2 epithelial cell transforming sequence 2 oncogene
    172. 55872 PBK PDZ binding kinase
    173. 55635 DEPDC1 DEP domain containing 1
    174. 11013 PMSL8 thymosin-like 8
    175. 259266 ASPM asp (abnormal spindle)-like, microcephaly
    associated (Drosophila)
    176. 10950 BTG3 BTG family, member 3
    177. 56992 KIF15 kinesin family member 15
    178. 29980 DONSON downstream neighbor of SON
    179. 5757 PTMA prothymosin, alpha (gene sequence 28)
    180. 5932 RBBP8 retinoblastoma binding protein 8
    181. 7903 ST8SIA4 ST8 alpha-N-neuramindine alpha-2,8-
    sialyltransferase 4
    182. 348235 FAM33A family with sequence similarity 33, member A
    183. 3182 HNRPAB heterogenous nuclear ribonucleoprotein A/B
    184. 3161 HMMR hyaluronan-mediated motility receptor (RHAHM)
    185. 5985 RFC5 replication factor C (activator 1) 5, 36.5 kDa
    186. 864 RUNX3 runt-related transcription factor 3
    187. 3930 LBR lamin B receptor
    188. 1434 CSE1L CSE1 chromosome segregation 1-like (yeast)
    189. 81610 C20orf129 chromosome 20 open reading frame 129
    190. 3146 HMGB1 high-mobility group box 1
    191. 55636 CHD7 chromodomain helicase DNA binding protein 7
    192. 54443 ANLN anillin, actin binding protein (scraps homolog,
    Drosophila)
    193. 5698 PSMB9 proteasome (prosome, macropain) subunit, beta
    type, 9 (large multifinctional protease 2)
    194. 7277 PUBA1 tubulin, alpha 1 (testis specific)
    195. 64282 PAPD5 PAP associated domain containing 5
    196. 201725 LOC201725 hypothetical protein LOC201725
    197. 7171 TPM4 tropomyosin 4
    198. 3838 KPNA2 jaryopherin alpha 2 (RAG cohort 1, importin alpha
    1)
    199. 116832 RPL39L ribosomal protein L39-like
    200. 4602 MYB v-myb myeloblastosis viral oncogene homolog
    (avian)
    201. 54962 FLJ20516 timeless-interacting protein
    202. 10541 ANP32B acidic (leucine-rich) nuclear phosphoprotein 32
    family, member B
    203. 9787 DLG7 discs, large homolog 7 (Drosophila)
    204. 147138 EVER2 epidermodysplasia verruciformis 2
    205. 157313 CDCA2 cell division cycle associated 2
    206. 11340 EXOSC8 exosome component 8
    207. 2956 MSH6 mutS homolog 6 (E. coli)
    208. 151246 SGOL2 shugoshin-like 2 (S. pombe)
    209. 27346 MAC30 hypothetical protein MAC30
    210. 5873 RAB27A RAB27A, member RAS oncogene family
    211. 79596 C13orf7 chromosome 13 open reading frame 7
    212. 10051 SMC4L1 SMC4 strctural maintenance of chromosome 4-
    like 1 (yeast)
    213. 3336 HSPE1 heat shock 10 kDa protein 1 (chaperonin 10)
    214. 6432 SFRS7 splicing factor, arginine/serine-rich 7, 35 kDa
    215. 8819 SAP30 sin3-associated polypeptide, 30 kDa
    216. 54801 FAM29A family with sequence similarity 29, member A
    217. 1123 CHN1 chimerin (chimaerin) 1
    218. 694 BTG1 B-cell translocation gene 1, anti-proliferative
    219. 153222 LOC153222 adult retina protein
    220. 3669 ISG20 interferon stimulated exonuclease gene 20 kDa
    221. 151556 GPR155 G protein-coupled receptor 155
    222. 6591 SNAI2 snail homolog 2 (Drosophila)
    223. 5920 RARRES3 retinoic acid receptor responder (tazarotene
    induced) 3
    224. 400172 LOC400172 similar ti KIAA1641 protein; melanoma-associated
    antigen; CLL-associated antigen KW-1
    225. 55281 FLJ11000 hypothetical protein FLJ11000
    226. 9783 RIMS3 regulating synaptic membrane exocytosis 3
    227. 6480 ST6GAL1 ST6 beta-galactosamide alpha-2,6-dialyltransferase 1
    228. 390 RND3 Rho family GTPase 3
    229. 10765 JARID1B Jumonji, AT rich interactive domain 1B (RBP2-like)
    230. 154091 SLC2A12 solute carrier familty 2 (facilitated glucose
    transporter), member 12
    231. 54981 C9orf95 chromosome 9 open reading frame 95
    232. 1663 DDX11 DEAD/H (asp-Glu-Ala-Asp/His) box polypeptide 11
    (CHL1-like helicase homolog, S. cerevisiae)
    233. 54800 DRE1 DRE1 protein
    234. 57515 TDE2 tumor differentially expressed 2
    235. 83719 YPEL3 yippee-like 3 (Drosophila)
    236. 5269 SERPINB6 serine (or cyesteine) proteinase inhibitor, clade B
    (ovalbumin), member 6
    237. 30061 SLC40A1 solute carrier family 40 (iron-regulated transporter),
    member 1
    238. 5660 PSAP prosaposin (variant Gaucher disease and variant
    metachromatic leukodystrophy)
    239. 51646 YPEL5 yippee-like 5 (Drosophila)
    240. 145788 FLJ27352 hypothetical LOC145788
    241. 81030 ZBP1 Z-DNA binding protein 1
    242. 57035 C1orf63 chromosome 1 open reading frame 63
    243. 9863 MAGI2 membrane associated guanylate kinase, WW and
    PDZ domain containing 2
    244. 9855 FARP2 FERM, RhoGEF and pleckstrin domain protein 2
    245. 57612 KIAA1466 KIAA1466 gene
    246. 56243 KIAA1217 KIAA1217
    247. 8365 HIST1H4H histone 1, H4h
    248. 440081 DDX12 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 12
    (CHL1-like helicase homolog, S. cerevisiae)
    249. 83937 RASSF4 Ras association (RalGDS/AF-6) domain family 4
    250. 56204 FLJ10980 hypothetical protein FLJ10980
    251. 22932 POMZP3 POM (POM121 homolog, rat) and ZP3 fusion
    252. 10628 TXNIP thioredoxin interacting protein
    253. 6720 SREBF1 sterol regulatory element binding transcription factor
    1
    254. 1508 CTSB cathepsin B
    255. 84513 HTPAP HTPAP protein
    256. 85352 KIAA1644 KIAA1644 protein
    257. 9388 LIPG lipase, endothelial
    258. 5163 PDK1 pyruvate dehydrogenase kinase, isoenzyme 1
    259. 23446 CDW92 CDW92 antigen
    260. 10156 RASA4 RAS p21 protein activator 4
    261. 23766 GABARAPL3 GABA(A) receptors associated protein like 3
    262. 56904 SH3GLB2 SH3-domain GRB2-like endophilin B2
    263. 6609 SMPD1 sphingomyelin phosphodiesterase 1, acid lysosomal
    (acid sphingomyelinase)
    264. 23259 DDHD2 DDHD domain containing 2
    265. 23092 ARHGAP26 Rho GTPase activating protein 26
    266. 27250 PDCD4 programmed cell death 4 (neoplastic transformation
    inhibitor)
    267. 3983 ABLIM1 actin binding LIM protein 1
    268. 23461 ABCA5 ATP-binding vassette, sub-family A (ABC1),
    member 5
    269. 4094 MAF v-maf nusculoaponeurotic fibrosomal oncogene
    homolog (avian)
    270. 23646 PLD3 phospholipase D family, member 3
    271. 51566 ARMCX3 armadillo repeat containing, X-linked 3
    272. 58476 TP53INP2 tumor protein p53 inducible nuclear protein 2
    273. 29994 BAZ2B bromodomain adjacent to zinc finger domain, 2B
    274. 283131 TncRNA trophoblast-derived noncoding RNA
    275. 4189 DNAJB9 DnaJ (Hsp40) homolog, subfamily B, member 9
    276. 9123 SLC16A3 solute carrier family 16 (monocarboxylic acid
    transporters), member 3
    277. 8473 OGT O-linked N-acetylglucosamine (GlcNAc) transferase
    (UDP-N-acetylglucosamine:polypeptide-N-
    acetylglucosaminyl transferase)
    278. 65018 PINK1 PTEN induced putative kinase 1
    279. 339448 LOC339448 hypothetical protein LOC339448
    280. 6513 SLC2A1 solute carrier family 2 (facilitated glucose
    transporter), member 1
    281. 3995 FADS3 faatty acid desaturase 3
    282. 155038 GIMAP8 GTPase, IMAP family member 8
    283. 90634 CG018 hypothetical geene CG018
    284. 55573 H41 hypothetical protein H41
    285. 9201 DCAMKL1 doublecortin and CaM kinase-like 1
    286. 388403 YPEL2 yippee-like 2 (Drosophila)
    287. 255631 COL24A1 collagen, type XXIV, alpha 1
    288. 8440 NCK2 NCK adaptor protein 2
    289. 81790 RNF170 ring finger protein 170
    290. 9706 ULK2 unc-51-like kinase 2 (C. elegans)
    291. 934 CD24 CD24 antigen (small cell lung carcinoma cluster 4
    antigen)
    292. 9532 BAG2 BCL2-associated anthanogene 2
    293. 23331 KIAA1043 KIAA1043 protein
    294. 10675 CSPG5 chondroitin sulfate proteoglycan 5 (neuroglycan C)
    295. 1102 RCBTB2 regulator of chromosome condensation (RCC1) and
    BTB (POZ) domain containing protein 2
    296. 2119 ETV5 ets variant gene 5 (ets-regulated molecule)
    297. 255488 IBRDC2 IBR domain containing 2
    298. 55076 TMEM45A transmembrane protein 45A
    299. 8364 HIST1H4C histone 1, H4c
    300. 3725 JUN v-jun sarcoma virus 17 oncogene homolog (avian)
    301. 384 ARG2 arginase, type II
    302. 10129 13CDNA73 hypothetical protein CG003
    303. 1960 EGR3 early growth response 3
    304. 27122 DKK3 dickkopf homolog 3 (Xenopus laevis)
    305. 11178 LZTS1 leucine zipper, putative tumor suppressor 1
    306. 143888 KDELC2 KDEL (Lys-Asp-Glu-Leu) containing 2
    307. 1601 DAB2 disabled homolog 2, mitogen-responsive
    phosphoprotein (Drosophila)
    308. 6542 SLC7A2 solute carrier family 7 (cationic amino acid
    transporter, y+ system), member 2
    309. 477 ATP1A2 ATPase, Na+/K+ transporting, aplha 2 (+)
    polypeptide
    310. 90161 HS6ST2 heparan sulfate 6-O-sulfotransferase 2
    311. 81031 SLC2A10 solute carrier family 2 (facilitated glucose
    transporter), member 10
    312. 56675 NRIP3 nuclear receptor interacting protein 3
    313. 1958 EGR1 early growth response 1
    314. 3714 JAG2 jagged 2
    315. 3897 L1CAM L1 cell adhesion molecule
    316. 1488 CTBP2 C-terminal binding protein 2
    317. 145173 B3GTL beta 3-glycosyltransferase-like
    318. 112399 EGLN3 egl nine homolog 3 (C. elegans)
    319. 22871 NLGN1 neuroligin 1
    320. 8804 CREG1 cellular repressor of E1A-stimulated genes 1
    321. 401081 FLJ22763 hypothetical gene supported by AK026416
    322. 25924 MYRIP myosin VIIA and Rab interacting protein
    323. 91694 FLJ23749 hypothetical protein FLJ23749
    324. 56155 TEX14 testis expressed sequence 14
    325. 1349 COX7B cytochrome c oxidase subunit VIIb
    326. 3695 ITGB7 integrin, beta 7
    327. 1164 CKS2 CDC28 protein kinase regulatory subunit 2
    328. 56919 DHX33 DEAH (Asp-Glu-Ala-His) box polypeptide 33
    329. 3276 HRMT1L2 HMT1 hnRNP methyltransferase-like 2 (S.
    cerevisiae)
    330. 116151 C20orf108 chromosome 20 open rading frame 108
    331. 25758 G2 G2 protein
    332. 25861 DFNB31 deafness, autosomal recessive 31
    333. 9666 DZIP3 zinc finger DAZ interacting protein 3
    334. 1486 CTBS chitobiase, di-N-acetyl-
    335. 3123 HLA-DRB1 major histocompatability complex, class II, DR beta 1
    336. 317649 EIF4E3 eukaryotic translation initiation factor 4E member 3
    337. 50854 C6orf48 chromosome 6 open reading frame 48
    338. 401024 FLJ44048 FLJ44048 protein
    339. 114327 EFHC1 EF-hand domain (C-terminal) containing 1
    340. 8334 HIST1H2AC histone 1, H2ac
    341. 284214 LOC284214 hypothetical protein LOC284214
    342. 10379 ISGF3G interferon-stimulated transcription factor 3, gamma
    48 kDa
    343. 113177 C19orf36 chromosome 19 open reading frame 36
    344. 56951 C5orf15 chromosome 5 open reading frame 15
    345. 285362 CUMF1 sulfatase modifying factor 1
    346. 3490 IGFBP7 insulin-like growth factor binding protein 7
    347. 1186 CLCN7 chloride channel 7
    348. 582 BBBS1 Bardet-Biedl syndrome 1
    349. 339456 LOC339456 hypothetical protein LOC339456
    350. 26115 DKFZO564D166 putative ankyrin-repeat containing protein
    351. 9895 KIAA0329 KIAA0329
    352. 1040 CDS1 CDP-fiacylglycerol synthase (phosphatidate
    cytidylyltransferase) 1
    353. 117854 TRIM6 tripartite motif-containing 6
    354. 3037 HAS2 hyaluronan synthase 2
    355. 4821 NKX2-2 NK2 transcription factor related, locus 2 (Drosophila)
    356. 26298 EHF ets homologous factor
    357. 22873 DZIP1 DAZ interacting protein 1
    358. 161742 SPRED1 sprouty-related, EVH1 domain containing 1
    359. 10052 GJA7 gap junction protein, alpha 7, 45 kDa (connexin 45)
    360. 79733 E2F8 E2F transcription factor B
    361. 10112 KIF20A kinesin family member 20A
    362. 54910 SEMA4C sema domain, immunoglobulin domain (lg),
    transmembrane domain (TM) and short cytoplasmic
    domain, (semaphorin) 4C
    363. 993 CDC25A cell division cycle 25A
    364. 3683 ITGAL integrin, alpha L (antigen CD11A (p180),
    lymphocyte function-associated antigen 1; alpha
    polypeptide)
    365. 9355 LHX2 LIM homobox 2
    366. 5578 PRKCA protein kinase C, aplha
    367. 157570 ESCO2 establishment of cohesion 1 homolog 2 (S.
    cerevisiae)
    368. 10252 SPRY1 sprouty homolog 1, antagonist of FGF signalling
    (Drosophila)
    369. 22998 KIAA1102 KIAA1102 protein
    370. 144455 E2F7 E2F transcription factor 7
    371. 2115 ETV1 ets variant gene 1
    372. 80144 FRAS1 Frase syndrome 1
    373. 1902 EDG2 endothelial differentiation, lysophosphatidic acid G-
    protein-coupled receptor, 2
    374. 148203 LOC148203 hypothetical protein LOC148203
    375. 8851 CDK5R1 cyclin-dependent kinase 5, regulatory subunit 1
    (p35)
    376. 28951 TRIB2 tribbles homolog 2 (Drosophila)
    377. 1491 CTH cystathionase (cystathionine gamma-lyase)
    378. 4281 MID1 midline 1 (Optiz/BBB syndrome)
    379. 145482 ZADH1 zinc binding alcohol dehydrogenase, domain
    containing 1
    380. 84858 ZNF503 zinc finger protein 503
    381. 55723 ASF1B ASF1 anti-silencing function 1 homolog B (S.
    cerevisiae)
    382. 1718 DHCR24 24-dehydrocholesterol reductase
    383. 1847 DUSP5 dual specificity phosphatase 5
    384. 64081 MAWBP MAWD binding protein
    385. 22822 PHLDA1 pleckstrin homology-like domain, family A, member
    1
    386. 389831 LOC389831 hypothetical gene supported by AL713796
    387. 9212 AURKB aurora kinase B
    388. 7272 TTK TTK protein kinase
    389. 84952 CGNL1 cingulin-like 1
    390. 150468 FLJ40629 hypothetical protein FLJ40629
    391. 23286 KIBRA KIBRA protein
    392. 29968 PSAT1 phosphoserine aminotransferase 1
    393. 8864 PER2 period homolog 2 (Drosophila)
    394. 4603 MYBL1 v-myb myeloblastosis viral oncogene homolog
    (avia)-like 1
    395. 285513 LOC285513 hypothetical protein LOC285513
    396. 64919 BCL11B B-cell CLL/lymphoma 11B (zinc finger protein)
    397. 83641 C10orf45 chromosome 10 open reading frame 45
    398. 6659 SOX4 SRY (sex determining region Y)-box 4
    399. 55964 3-Sep septin 3
    400. 80150 ASRGL1 asparaginase like 1
    401. 8630 HSD17B6 hydroxysteroid (17-beta) dehydrogenase 6
    402. 7004 TEAD6 TEA domain family member 4
    403. 8871 SYNJ2 synaptojanin 2
    404. 56935 FN5 FN5 protein
    405. 51232 CRIM1 cysteine-rich motor neuron 1
    406. 493861 EID3 E1A-like inhibitor of differentiation 3
    407. 2983 GUCY1B3 guanylate cyclase 1, soluble, beta 3
    408. 51776 ZAK sterile alpha motif and leucine zipper containing
    kinase AZK
    409. 9953 HS3ST3B1 heparan sulfate (glucosamine) 3-O-sulfotransferase
    3B1
    410. 23310 hCAP-D3 KIAA0056 protein
    411. 2326 FMO1 flavin containing monooxygenase 1
    412. 51063 FAM26B family with sequence similarity 26, member B
    413. 1038 CDR1 cerebellar degeneration-related protein 1, 34 kDa
    414. 4325 MMP16 matrix metalloproteinase 16 (membrane-inserted)
    415. 55247 NEIL3 nei endonuclease VIII-like 3 (E. coli)
    416. 91607 FLJ34922 hypothetical protein FLJ34922
    417. 284801 LOC284801 hypothetical protein LOC284801
    418. 5641 LGMN legumain
    419. 4121 MAN1A1 mannosidase, alpha, class 1A, member 1
    420. 1414 CRYBB1 crystallin, beta B1
    421. 8530 CST7 cystatin F (leukocystatin)
    422. 2669 GEM GTP binding protein overexpressed in skeletal
    muscle
    423. 126731 C1orf96 chromosome 1 open reading frame 96
    424. 26095 PTPN20 protein tyrosine phosphatase, non-receptor type 20
    425. 57037 ANKMY2 ankyrin repeat and MYND domain containing 2
    426. 3708 ITPR1 inositol 1,4,5-triphosphate receptor, type 1
    427. 55740 ENAH enabled homolog (Drosphila)
    428. 57761 TRIB3 tribbles homolog 3 (Drosophila)
    429. 6867 TACC1 transforming, acidic coiled-coil containing protein 1
    430. 27115 PDE7B phosphodiesterase 7B
    431. 5361 PLXNA1 plexin A1
    432. 54908 FLJ20364 hypothetical protein FLJ20364
    433. 79710 MORC4 MORC family CW-type zinc finger 4
    434. 399664 RKHD1 ring finger and KH domain containing 1
    435. 90390 THRAP6 thyroid hormone receptor associated protein 6
    436. 2767 GNA11 guanine nucleotide binding protein (G protein),
    alpha 11 (Gq class)
    437. 5793 PTPRG protein tyrosine phosphatase, receptor type, G
    438. 6385 SDC4 syndecan 4 (amphiglycan, ryudocan)
    439. 205 AK3L1 adenylate kinase 3-like 1
    440. 490 ATP2B1 ATPase, Ca++ transporting, plasma membrane 1
    441. 2026 ENO2 enolase 2 (gamma, neuronal)
    442. 23046 KIF21B kinesin family member 21B
    443. 60468 BACH2 BTB and CNC homology 1, basic leucine zipper
    transcription factor 2
    444. 55013 FLJ20647 hypothetical protein FLJ20647
    445. 256435 ST6GALNAC3 ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-
    galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-
    sialyltransferase 3
    446. 6611 SMS spermine synthase
    447. 79037 MGC2463 hypothetical protein MGC2463
    448. 23279 NUP160 nucleoporin 160 kDa
    449. 10160 FARP1 FERM, RhoGEF (ARHGEF) and pleckstrin domain
    protein 1 (chondrocyte-derived)
    450. 6877 TAF5 TAF5 RNA polymerase II, TATA box binding protein
    (TBP)-associated factor, 100 kDa
    451. 2534 FYN FYN oncogene related to SRC, FGR, YES
    452. 23531 MMD monocyte to macrophage differentiation-associated
    453. 79621 FLJ11712 hypothetical protein FLJ11712
    454. 29899 GPSM2 G-protein signalling modulator 2 (AGS3-like, C.
    elegans)
    455. 53354 PANK1 pantothenate kinase 1
    456. 2047 EPHB1 EPH receptor B1
    457. 6558 SLC12A2 solute carrier family 12 (sodium/potassium/chloride
    transporters), member 2
    458. 8502 PKP4 plakophilin 4
    459. 116496 C1orf24 chromosome 1 open reading frame 24
    460. 84314 MGC10744 hypothetical protein MGC10744
    461. 54830 FLJ20130 hypothetical protein FLJ20130
    462. 10602 CDC42EP3 CDC42 effector protein (Rho GTPase binding) 3
    463. 55257 C20orf20 chromosome 20 open reading frame 20
    464. 4885 MPTX2 neuronal pentraxin II
    465. 8317 CDC7 CDC7 cell division cycle 7 (S. cerevisiae)
    466. 55816 DOK5 docking protein 5
    467. 82732 RIOK1 RIO kinase 1 (yeast)
    468. 489 ATP2A3 ATPase, Ca++ transporting, ubiquitous
    469. 83990 BRIP1 BRCA1 interacting protein C-terminal helicase 1
    470. 9295 SFRS11 splicing factor, arginine/serine-rich 11
    471. 55166 C6orf139 chromosome 6 open reading frame 139
    472. 119467 HGC32871 hypothetical protein MGC32871
    473. 54101 RIPK4 receptor-interacting serine-threonine kinase 4
    474. 241 ALOX5AP arachidonate 5-lipoxygenase-activating protein
    475. 2104 ESRRG estrogen-related receptor gamma
    476. 6574 SLC20A1 solute carrier family 20 (phosphate transporter),
    member 1
    477. 960 CD44 CD44 antigen (homing function and indian blood
    group system)
    478. 26031 OSBPL3 oxysterol binding protein-like 3
    479. 23646 NUP62 nucleoporin 62 kDa
    480. 9448 MAP4K4 mitogen-activated protein kinase kinase kinase
    kinase 4
    481. 26084 SGEF Src homology 3 domain-containing guanine
    nucleotide exchange factor
    482. 9735 KNTC1 kinetochore associated 1
    483. 84803 MGC11324 hypothetical protein MGC11324
    484. 81839 VANGL1 vang-like 1 (van gogh, Drosophila)
    485. 9734 HDAC9 histone deacetylase 9
    486. 51703 ACSL5 acyl-CoA synthetase long-chain family member 5
    487. 10155 TRIM28 tripartite motif-containing 28
    488. 54566 EPB41L4B erythrocyte membrane protein band 4.1 like 4B
    489. 10019 LNK lymphocyte adaptor protein
    490. 4082 MARCKS myristoylated alanine-rich protein kinase C
    substrate
    491. 23012 STK38L serine/threonine kinase 38 like
    492. 9759 HDAC4 histone deacetylase 4
    493. 657 BMPR1A bone morphogenetic protein receptor, type IA
    494. 22837 COBLL1 COBL-like 1
    495. 79888 FLJ12443 hypothetical protein FLJ12443
    496. 79154 MGC4172 chort-chain dehydrogenase/reductase
    497. 4076 M11S1 membrane component, chromosome 11, surface
    marker 1
    498. 79930 DOK3 docking protein 3
    499. 4086 SMAD1 SMAD, mothers against DPP homolog 1
    (Drosophila)
    500. 79180 EFHD2 EF hand domain family, member D2
    501. 6340 SCNN1G sodium channel, nonvoltage-gated 1, gamma
    502. 51015 ISOC1 isochorismatase domain containing 1
    503. 6999 TDO2 tryptophan 2,3-dioxygenase
    504. 55276 PGM2 phosphoglucomutase 2
    505. 55270 NUDT15 nudix (nucleoside diphosphate linked moiety X)-type
    motif 15
    506. 51174 TUBD1 tubulin, delta 1
    507. 1789 DNMT3B DNA (cytosine-5-)-methyltransferase 3 beta
    508. 84451 KIAA1804 mixed lineage kinase 4
    509. 5036 PA2G4 proliferation-associated 2G4, 38 kDa
    510. 11177 BAZ1A bromodomain adjacent to zinc finger domain, 1A
    511. 158563 LOC158563 hypothetical protein LOC158563
    512. 4957 ODF2 outer dense fiber of sperm tails 2
    513. 89891 WDR34 WD repeat domain 34
    514. 4640 MYO1A myosin IA
    515. 26018 LRIG1 leucine-rich repeates and immunoglobulin-like
    domains 1
    516. 9738 CP110 CP110 protein
    517. 278708 APITD1 apoptosis-inducing, TAF9-like domain 1
    518. 56952 PRTFDC1 phosphoribosyl transferase domain containing 1
    519. 3099 HK2 hexokinase 2
    520. 200894 ARL2L1 ADP-ribosylation factor-like 2-like 1
    521. 10625 IVNS1ABP influenza virus NS1A binding protein
    522. 10436 C2F C2f protein
    523. 79038 ZFYVE21 zinc finger, FYVE domain containing 21
    524. 7091 TLE24 transducin-like enhancer of split 4 (E(sp1) homolog,
    Drosophila)
    525. 7291 TWIST1 twist homolog 1 (acrocephalosyndactyly 3; Saethre-
    Chotzen syndrome) (Drosophila)
    526. 87 ACTN1 actinin, alpha 1
    527. 1736 DKC1 dyskeratosis congenita 1, dyskerin
    528. 10265 IRX5 iroquois homeobox protein 5
    529. 8553 BHLHB2 basic helix-loop-helix domain containing, class B, 2
    530. 54947 FLJ20481 hypothetical protein FLJ20481
    531. 5150 PDE7A phosphodiesterase 7A
    532. 83857 ARG99 ARG99 protein
    533. 7791 ZYX zyxin
    534. 27131 SNX5 sorting nexin 5
    535. 9112 MTA1 metastasis associated 1
    536. 80014 BOMB BH3-only member B protein
    537. 139886 LOC139886 hypothetical protein LOC139886
    538. 3189 HNRPH3 heterogeneous nuclear ribonucleoprotein H3 (2H9)
    539. 56905 DKFZP434H132 DKFZP434H132 protein
    540. 10838 ZNF275 zinc finger protein 275
    541. 11118 MTN3A2 butyrophilin, subfamily 3, member A2
    542. 401505 C9orf105 chromosome 9 open reading frame 105
    543. 1-0384 BTN3A3 butyrophilin, subfamily 3, member A3
    544. 8566 PDXK pyridoxal (pyridoxine, vitamin B6) kinase
    545. 10098 TSPAN5 tetraspanin 5
    546. 6526 SLC5A3 solute carrier family 5 (inositol transporters),
    member 3
    547. 6711 SPTBN1 spectrin, beta, non-erythrocytic 1
    548. 26010 DNAPTP6 DNA polymerase-transactivated protein 6
    549. 84108 LCGF6 polycomb group ring finger 6
    550. 51444 RNF138 ring finger protein 138
    551. 23089 PEG10 paternally expressed 10
    552. 22995 Cep152 KIAA0912 protein
    553. 1503 CTPS CTP synthase
    554. 6302 SAS sarcoma amplified sequence
    555. 3956 LGALS1 lectin, galactoside-binding ssoluble, 1 (galectin 1)
    556. 126823 KARCA1 kelch/ankyrin repeat containing cyclin A1 interacting
    protein
    557. 8605 PLA2G4C phospholipase A2, group IVC (cytosolic, calcium-
    independent)
    558. 84981 MGC14376 hypothetical protein MGC14376
    559. 9120 SLC16A6 solute carrier family 16 (monocarboxylic acid
    transporters), member 6
    560. 5816 PVALB parvalbumin
    561. 115294 LOC115294 similar to hypothetical protein FLJ10883
    562. 8986 NOL3 nucleolar protein 3 (apoptosis repressor with CARD
    domain)
    563. 3055 HCK hemopoietic cell kinase
    564. 339803 LOC339803 hypothetical protein LOC339803
    565. 252839 TMEM9 transmembrane protein 9
    566. 2982 GUCY1A3 guanylate cyclase 1, soluble, alpha 3
    567. 706 BZRP benzodiazapeine receptor (peripheral)
    568. 5797 PTPRM protein tyrosine phosphatase, receptor type, M
    569. 9961 MVP major vault protein
    570. 999 CDH1 cadherin 1, type 1, E-cadherin (epithelial)
    571. 2537 G1P3 interferon, alpha-inducible protein (clone IFI-6-16)
    572. 94103 ORMDL3 ORM1-like 3 (S. cerevisiae)
    573. 8337 HIST2H2AA histone 2, H2aa
    574. 10057 ABCC5 ATP-binding cassette, sub-family C (CFTR/MRP),
    member 5
    575. 5274 SERPINI1 serine (or cyesteine) proteinase inhibitor, clade I
    (neuroserpin), member 1
    576. 3358 HTRC2 5-hydroxytryptamine (serotonin) receptor 2C
    577. 158158 RASEF RAS and EF hand domain containing
    578. 304 ANXA2P2 annexin A2 pseudogene 2
    579. 7259 TSPYL1 TSPY-like 1
    580. 8878 SQSTM1 sequestosome 1
    581. 7494 XBP1 X-box binding protein 1
    582. 302 ANXA2 annexin A2
    583. 4864 NPC1 Nielmann-Pick disease, type C1
    584. 8780 RIOK3 RIO kinase 3 (yeast)
    585. 27319 BHLHB5 basic helix-loop-helix domain containing, class B, 5
    586. 55827 IQWD1 IQ motif and WD repeats 1
    587. 966 CD59 CD59 antigen p18-20 (antigen identified by
    monoclonal antobodies 16.3A5, EJ16, EJ30, EL32
    and G344)
    588. 55830 GLT8D1 glycosyltransferase 8 domain containing 1
    589. 25934 NIPSNAP3A nipsnap homolog 3A (C. elegans)
    590. 9451 EIF2AK3 eukaryotic translation initiation factor 2-alpha kinase
    3
    591. 80267 C1orf22 chromosome 1 open reading frame 22
    592. 754 PTTG1IP pituitary tumor-transforming 1 interacting protein
    593. 9236 CCPG1 cell cycle progression 1
    594. 6773 STAT2 signal transducer and activator of transcription 2,
    113 kDa
    595. 90701 SEC11L3 SEC11-like 3 (S. cerevisiae)
    596. 2590 GALNT2 UDP-N-acetyl-alpha-D-galactosamine:polypeptide
    N-acetylgalactosaminyltransferase 2 (GalNAc-T2)
    597. 25976 TIPARP TCDD-inducible poly(ADP-ribose) polymerase
    598. 57674 C17orf27 chromosome 17 open reading frame 27
    599. 7844 RNF103 ring finger protein 103
    600. 93953 ACRC acidic repeat containing
    601. 6990 TCTE1L t-complex-associated-testis-expressed 1-like
    602. 571 BACH1 BTB and CNC homology 1, basic leucine zipper
    transcription factor 1
    603. 6672 SP100 nuclear antigen Sp100
    604. 2799 GNS glucosamine (N-acetyl)-6-sulfatase (Sanfilippo
    disease IIID)
    605. 10550 ARL6IP5 ADP-ribosylation-like factor 6 interacting protein 5
    606. 79738 FLJ23560 hypothetical protein FLJ23560
    607. 54059 C21orf57 chromosome 21 open reading frame 57
    608. 3275 HRMT1L1 HMT1 hnRNP methyltransferase-like 1 (S.
    cerevisiae)
    609. 51706 NQO3A2 NAD(P)H:quinoline oxidoreductase type 3,
    polypeptide A2
    610. 79185 MGC4170 MGC4170 protein
    611. 80315 CPEB4 cytoplasmic polyadenylation element binding protein
    4
    612. 3982 LIG4 ligase IV, DNA, ATP-dependent
    613. 1299 COL9A3 collagen, type IX, alpha 3
    614. 3572 IL6ST interleukin 6 signal transducer (gp130, oncostatin M
    receptor)
    615. 107 ADCY1 adenylate cyclase 1 (brain)
    616. 84181 CHD6 chromodomain helicase DNA binding protein 6
    617. 54431 DNAJC10 DnaJ (Hsp40) homolog, subfamily C, member 10
    618. 283846 DKFZP547E087 PI-3-kinase-related kinase SMG-1-like
    619. 25796 PGLS 6-phosphogluconolactonase
    620. 5800 PTPRO protein tyrosine phosphotase, receptor type, O
    621. 5476 PPGB protective protein for beta-glactosidase
    (galactosialidosis)
    622. 54885 FLJ20298 FLJ20298 protein
    623. 1368 CPM carboxypeptidase M
    624. 586 BCAT1 branched chain aminotransferase 1, cytosolic
    625. 130271 PLEKHH2 pleckstrin homology domain containing, family H
    (with MyTH4 domain) member 2
    626. 81930 KIF18A kinesin family member 18A
    627. 11096 ADAMTS5 a disintegrin-like and metalloprotease (reprolysin
    type) with thrombospondin type 1 motif, 5
    (aggrecanase-2)
    628. 4148 MATN3 matrilin 3
    629. 56121 PCDHB15 photocadherin beta 15
    630. 57552 AADACL1 arylacetamide deacetylase-like 1
    631. 64396 GMCL1L germ cell-less homolog 1 (Drosophila)-like
    632. 3119 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1
    633. 1827 DSCR1 Down syndrome critical region gene 1
    634. 3202 HOXA5 homeo box A5
    635. 3298 HSF2 heat shock transcription factor 2
    636. 387914 TMEM46 transmembrane protein 46
    637. 11169 WDHD1 WD repeat and HNG-box DNA binding protein 1
    638. 79899 FLJ14213 hypothetical protein FLJ14213
    639. 1400 CRMP1 collapsin response mediator protein 1
    640. 55117 SLC6A15 solute carrier family 6, member 15
    641. 134429 STARD4 START domain containing 4, sterol regulated
    642. 253832 ZDHHC20 zinc finger, DHHC-type containing 20
    643. 84986 ARHGAP19 Rho GTPase activating protein 19
    644. 5050 PAFAH1B3 platelet-activating factor acetylhydrolase, isoform Ib,
    gamma subunit 29 kDa
    645. 4208 MEF2C MADS box transcription enhancer factor 2,
    polypeptide C (myocyte enhancer factor 2C)
    646. 9994 CAP8AP2 CASP8 associated protein 2
    647. 5634 PRPS2 phosphoribosyl pyrophosphate synthetase 2
    648. 23587 DEP6 S-phase 2 protein
    649. 57685 KIAA1573 KIAA1573 protein
    650. 57530 CGN cingulin
    651. 1633 DCK deoxycytidine kinase
    652. 24147 FJX1 four jointed box 1 (Drosophila)
    653. 9882 TBC1D4 TBC1 domain family, member 4
    654. 55183 RIF1 RAP1 interacting factor homolog (yeast)
    655. 221362 LOC221362 hypothetical protein LOC221362
    656. 5569 PKIA protein kinase (cAMP-dependent, catalytic) inhibitor
    alpha
    657. 6891 TAP2 transporter 2, ATP-binding cassette, sub-family B
    (MDR/TAP)
    658. 11252 PACSIN2 protein kinase C and casein kinase substrate in
    neurons 2
    659. 81575 DKFZP434F0318 hypothetical protein DKFZp434F0318
    660. 56909 THAP10 THAP domain containing 10
    661. 55110 FLJ10292 mago-nashi homolog
    662. 9612 NCOR2 nuclear recxeptor co-repressor 2
    663. 257415 MGC40405 hypothetical protein MGC40405
    664. 160897 ITR intimal thickness-related receptor
    665. 4668 NAGA N-acetylgalactosamidase, alpha-
    666. 84890 C10orf22 chromosome 10 open reading frame 22
    667. 2618 GART phosphoribosylglycinamide formyltransferase,
    phosphoribosylglycinamide synthetase,
    phosphoribosylaminoimidazole synthetase
    668. 80210 FLJ12584 melanoma/melanocyte specific protein KU-MEL-1
    669. 57534 MIB1 mindbomb homolog 1 (Drosophila)
    670. 56122 PCDHB14 protocadherin beta 14
    671. 10966 RAB40B RAB40B, member RAS oncogene family
    672. 5095 PCCA propionyl Coenzyme A carboxylase, alpha
    polypeptide
    673. 55857 C20orf19 chromosome 20 open reading frame 19
    674. 285464 FLJ34443 hypothetical protein FLJ34443
    675. 1509 CTSD cathepsin D (lyosomal aspartyl protease)
    676. 91614 LOC91614 nocel 58.3 kDa protein
    677. 2200 FBN1 fibrillin 1 (Marfan syndrome)
    678. 6347 CCL2 chemokine (C-C motif) ligand 2
    679. 2743 GLRB glyceine receptor, beta
    680. 116448 OLIG1 oligodendrocyte transcription factor 1
    681. 3613 IMPA2 inositol(myo)-1(or 4)-monophosphastase 2
    682. 6764 ST5 suppression of tumorigenicity 5
    683. 4137 MAPT microtubule-associated protein tau
    684. 9099 USP2 ubiquitin specific protease 2
    685. 5777 PTPN6 protein tyrosine phosphatase, non-receptor type 6
    686. 59338 PLEKHA1 pleckstrin homology domain containing, family A
    (phosphoinositide binding specific) member 1
    687. 1028 CDKN1C cyclin-dependent kinase inhibitor 1C (p57, Kip2)
    688. 2177 FANCD2 Fanconi anemia, complementation group D2
    689. 165055 FLJ32745 hypothetical protein FLJ32745
    690. 151827 LRRC34 leucine rich repeat containing 34
    691. 203562 TMEM31 transmembrane protein 31
    692. 6934 TCF7L2 transcription factor 7-like 2 (T-cell specific, HMG-
    box)
    693. 5577 PRKAR2B protein kinase, cAMP-dependent, regulatory, type II,
    beta
    694. 79442 LRRC2 leucine rich repeat containing 2
    695. 55366 LGR4 leucine-rich repeat-containing G protein-coupled
    receptor 4
    696. 7975 MAFK v-maf musculoaponeurotic fibrosarcoma oncogene
    homolog K (avian)
    697. 340252 ZNF680 zinc finger protein 680
    698. 22800 RRAS2 related RAS viral (r-ras) oncogene homolog 2
    699. 2730 GCLM glutamate-cysteine ligase, modifier subunit
    700. 29841 GRHL1 grainyhead-like 1 (Drosophila)
    701. 9214 FAIM3 Fas apoptotic inhibitory molecule 3
    702. 57406 ABHD6 abhydrolase domain containing 6
    703. 4660 PPP1R12B protein phosphatase 1, regulatory (inhibitor) subunit
    12B
    704. 157503 LOC157503 hypothetical protein LOC157503
    705. 285704 RGMB RGM domain family, member B
    706. 55614 C20orf23 chromosome 20 open reading frame 23
    707. 85463 ZC3H12C zinc finger CCCH-type containing 12C
    708. 6470 SHMT1 serine hydroxymethyltransferase 1 (soluble)
    709. 9397 NMT2 N-myristoyltransferase 2
    710. 201161 PRR6 proline rich 6
    711. 8564 KMO kynurenine 3-monooxygenase (kynurenine 3-
    hydroxylase)
    712. 283824 LOC283824 hypothetical protein LOC283824
    713. 57522 SRGAP1 SLIT-ROBO Rho GTPase activating protein 1
    714. 79695 GALNT12 UDP-N-acetyl-alpha-D-galactosamine:polypeptide
    N-acetylgalactosaminyltransferase 12 (GalNAc-T12)
    715. 396 ARHGDIA Rho GDP dissociation inhibitor (GDI) alpha
    716. 9208 LRRFIP1 leucine rich repeat (in FLII) interacting protein 1
    717. 6453 ITSN1 intersectin 1 (SH3 domain protein)
    718. 169200 DKFZp762C1112 hypothetical protein DKFZp762C1112
    719. 9331 B4GALT6 UDP-Gal:betaGlcNAc beta 1,4-
    galactosyltransferase, polypeptide 6
    720. 8458 TTF2 transcription termination factor, RNA polymerase II
    721. 1047 CLGN calmegin
    722. 93949 CXorf10 chromosome X open reading frame 10
    723. 51762 RAB8B RAB8B, member RAS oncogene family
    724. 5267 SERPINA4 serine (or cysteine) proteinase inhibitor, clade A
    (alpha-1 antiproteinase, antitrypsin), member 4
    725. 1844 DISP2 dual spoecificity phosphatase 2
    726. 79720 FLJ12750 hypothetical protein FLJ12750
    727. 4522 MTHFD1 methylenetetrahydrofolase dehydrogenase (NADP+
    dependent) 1, methenyltetrahydrofolate
    cyclohydeolase, formyltetrahydrofolate synthetase
    728. 5198 PFAS phosphoribosylformylglycinamidine synthase (FGAR
    amidotransferase)
    729. 55544 RNPC1 RNA-binding region (RNP1, RRM) containing 1
    730. 9261 MAPKAPK2 mitogen-activated protein kinase-activated protein
    kinase 2
    731. 285761 DCBLD1 discoidin, CUB and LCCL domain containing 1
    732. 161527 LOC161527 hypothetical protein LOC161527
    733. 8548 BLZF1 basic leucine zipper nuclear factor 1 (JEM-1)
    734. 10537 UBD ubiquitin D
    735. 64224 FLJ22313 hypothetical protein FLJ22313
    736. 4637 MYL6 myosin, light polypeptide 6, alkali, smooth muscle
    and non-muscle
    737. 51569 UFM1 ubiquitin-fold modifier 1
    738. 57599 WDR48 WD repeat domain 48
    739. 57162 PELI1 pellino homolog 1 (Drosophila)
    740. 58486 LOC58486 transposon-derived Buster1 transposase-like protein
    gene
    741. 1266 CNN3 calponin 3, acidic
  • TABLE III
    ENTREZ
    GENE ID GENE SYMBOL GENE DESCRIPTION
    1. 6348 CCL3 chemokine (C-C motif) ligand 3
    2. 55388 MCM10 MCM10 minichromosome maintenance deficient 10
    (S. cerevisiae)
    3. 7117 TMSL3 thymosin-like 3
    4. 1017 CDK2 cyclin-dependent kinase 2
    5. 79019 C22orf18 chromosome 22 open reading frame 18
    6. 6241 RRM2 ribonucleotide reductase M2 polypeptide
    7. 4605 MYBL2 v-myb myeloblastosis viral oncogene homolog
    (avian)-like 2
    8. 894 CCND2 cyclin D2
    9. 57405 SPBC25 spindle pole body component 25 homolog (S. cerevisiae)
    10. 146909 LOC146909 hypothetical protein LOC146909
    11. 150271 LOC150271 hypothetical protein LOC150271
    12. 203 AK1 adenylate kinase 1
    13. 4050 LTB lymphotoxin beta (TNF superfamily, member 3)
    14. 257019 FRMD3 FERM domain containing 3
    15. 8357 HIST1H3H histone 1, H3h
    16. 23710 GABARAPL1 GABA(A) receptor-associated protein like 1
    17. 9201 DCAMKL1 doublecortin and CaM kinase-like 1
    18. 934 CD24 CD24 antigen (small cell lung carcinoma cluster 4
    antigen)
    19. 9532 BAG2 BCL2-associated athanogene 2
    20. 23331 KIAA1043 KIAA1043 protein
    21. 10675 CSPG5 chondroitin sulfate proteoglycan 5 (neuroglycan C)
    22. 1102 RCBTB2 regulator of chromosome condensation (RCC1) and
    BTB (POZ) domain containing protein 2
    23. 2119 ETV5 ets variant gene 5 (ets-related molecule)
    24. 255488 IBRDC2 IBR domain containing 2
    25. 55076 TMEM45A transmembrane protein 45A
    26. 8364 HIST1H4C histone 1, H4c
    27. 3725 JUN v-jun sarcoma virus 17 oncogene homolog (avian)
    28. 384 ARG2 arginase, type II
    29. 10129 13CDNA73 hypothetical protein CG003
    30. 1960 EGR3 early growth response 3
    31. 27122 DKK3 dickkopf homolog 3 (Xenopus laevis)
    32. 11178 LZTS1 leucine zipper, putative tumor suppressor 1
    33. 143888 KDELC2 KDEL (Lys-Asp-Glu-Leu) containing 2
    34. 1601 DAB2 disabled homolog 2, mitogen-responsive
    phosphoprotein (Drosophila)
    35. 6542 SLC7A2 solute carrier family 7 (cationic amino acid
    transporter, y+ system), member 2
    36. 477 ATP1A2 ATPase, Na+/K+ transporting, alpha 2 (+)
    polypeptide
    37. 90161 HS6ST2 heparan sulfate 6-O-sulfotransferase 2
    38. 81031 SLC2A10 solute carrier family 2 (facilitated glucose
    transporter), member 10
    39. 56675 NRIP3 nuclear receptor interacting protein 3
    40. 1958 EGR1 early growth response 1
    41. 3714 JAG2 jagged 2
    42. 3897 L1CAM L1 cell adhesion molecule
    43. 1488 CTBP2 C-terminal binding protein 2
    44. 145173 B3GTL beta 3-glycosyltransferase-like
    45. 112399 EGLN3 egl nine homolog 3 (C. elegans)
    46. 22871 NLGN1 neuroligin 1
    47. 8804 CREG1 cellular repressor of E1A-stimulated genes 1
    48. 117854 TRIM6 tripartite motif-containing 6
    49. 3037 HAS2 hyaluronan synthase 2
    50. 4821 NKX2-2 NK2 transcription factor related, locus 2
    (Drosophila)
    51. 26298 EHF ets homologous factor
    52. 22873 DZIP1 DAZ interacting protein 1
    53. 161742 SPRED1 sprouty-related, EVH1 domain containing 1
    54. 10052 GJA7 gap junction protein, alpha 7, 45 kDa (connexin 45)
    55. 79733 E2F8 E2F transcription factor 8
    56. 10112 KIF20A kinesin family member 20A
    57. 54910 SEMA4C sema domain, immunoglobulin domain (Ig),
    transmemebrane domain (TM) and short cytoplasmic
    domain, (semaphorin) 4C
    58. 993 CDC25A cell division cycle 25A
    59. 3683 ITGAL integrin, alpha L (antigen CD11A (p180),
    lymphocyte function-associated antigen 1; alpha
    polypeptide)
    60. 9355 LHX2 LIM homeobox 2
    61. 5578 PRKCA protein kinase C, alpha
    62. 157570 ESCO2 establishment of cohesion 1 homolog 2 (S. cerevisiae)
    63. 10252 SPRY1 sprouty homolog 1, antagonist of FGF signaling
    (Drosophila)
    64. 22998 KIAA1102 KIAA1102 protein
    65. 144455 E2F7 E2F transcription factor 7
    66. 2115 ETV1 ets variant gene 1
    67. 80144 FRAS1 Fraser syndrome 1
    68. 1902 EDG2 endothelial differentiation, lysophosphatidic acid G-
    protein-coupled receptor, 2
    69. 148203 LOC148203 hypothetical protein LOC148203
    70. 8851 CDK5R1 cyclin-dependent kinase 5, regulatory subunit 1
    (p35)
    71. 28951 TRIB2 tribbles homolog 2 (Drosophila)
    72. 1491 CTH cystathionase (cystathionine gamma-lyase)
    73. 4281 MID1 midline 1 (Opitz/BBB syndrome)
    74. 145482 ZADH1 zinc binding alcohol dehydrogenase, domain
    containing 1
    75. 84858 ZNF503 zinc finger protein 503
    76. 55723 ASF1B ASF1 anti-silencing function 1 homolog B (S. cerevisiae)
    77. 1718 DHCR24 24-dehydrocholesterol reductase
    78. 1847 DUSP5 dual specificity phosphatase 5
    79. 64081 MAWBP MAWD binding protein
    80. 22822 PHLDA1 pleckstrin homology-like domain, family A, member 1
    81. 389831 LOC389831 hypothetical gene supported by AL713796
    82. 9212 AURKB aurora kinase B
    83. 7272 TTK TTK protein kinase
    84. 84952 CGNL1 cingulin-like 1
    85. 150468 FLJ40629 hypothetical protein FLJ40629
    86. 23286 KIBRA KIBRA protein
    87. 29968 PSAT1 phosphoserine aminotransferase 1
    88. 8864 PER2 period homolog 2 (Drosophila)
    89. 4603 MYBL1 v-myb myeloblastosis viral oncogene homolog
    (avian)-like 1
    90. 285513 LOC285513 hypothetical protein LOC285513
    91. 64919 BCL11B B-cell CLL/lymphoma 11B (zinc finger protein)
    92. 83641 C10orf45 chromosome 10 open reading frame 45
    93. 6659 SOX4 SRY (sex determining region Y)-box 4
    94. 55964 3-Sep septin 3
    95. 80150 ASRGL1 asparaginase like 1
    96. 8630 HSD17B6 hydroxysteroid (17-beta) dehydrogenase 6
    97. 7004 TEAD4 TEA domain family member 4
    98. 8871 SYNJ2 synaptojanin 2
    99. 56935 FN5 FN5 protein
    100. 51232 CRIM1 cysteine-rich motor neuron 1
    101. 493861 EID3 E1A-like inhibitor of differentiation 3
    102. 2983 GUCY1B3 guanylate cyclase 1, soluble, beta 3
    103. 51776 ZAK sterile alpha motif and leucine zipper containing
    kinase AZK
    104. 9953 HS3ST3B1 heparan sulfate (glucosamine) 3-O-sulfotransferase
    3B1
    105. 23310 hCAP-D3 KIAA0056 protein
    106. 2326 FMO1 flavin containing monooxygenase 1
    107. 51063 FAM26B family with sequence similarity 26, member B
    108. 1038 CDR1 cerebellar degeneration-related protein 1, 34 kDa
    109. 4325 MMP16 matrix metalloproteinase 16 (membrane-inserted)
    110. 55247 NEIL3 nei endonuclease VIII-like 3 (E. coli)
    111. 91607 FLJ34922 hypothetical protein FLJ34922
    112. 284801 LOC284801 hypothetical protein LOC284801
    113. 5641 LGMN legumain
    114. 4121 MAN1A1 mannosidase, alpha, class 1A, member 1
    115. 1414 CRYBB1 crystallin, beta B1
    116. 54885 FLJ20298 FLJ20298 protein
    117. 1368 CPM carboxypeptidase M
    118. 586 BCAT1 branched chain aminotransferase 1, cytosolic
    119. 130271 PLEKHH2 pleckstrin homology domain containing, family H
    (with MyTH4 domain) member 2
    120. 81930 KIF18A kinesin family member 18A
    121. 11096 ADAMTS5 a disintegrin-like and metalloprotease (reprolysin
    type) with thrombospondin type 1 motif, 5
    (aggrecanase-2)
    122. 4148 MATN3 matrilin 3
    123. 56121 PCDHB15 protocadherin beta 15
    124. 57552 AADACL1 arylacetamide deacetylase-like 1
    125. 91614 LOC91614 novel 58.3 KDA protein
    126. 2200 FBN1 fibrillin 1 (Marfan syndrome)
    127. 6347 CCL2 chemokine (C-C motif) ligand 2
    128. 2743 GLRB glycine receptor, beta
    129. 116448 OLIG1 oligodendrocyte transcription factor 1
    130. 3613 IMPA2 inositol(myo)-1(or 4)-monophosphatase 2
    131. 6764 ST5 suppression of tumorigenicity 5
    132. 4137 MAPT microtubule-associated protein tau
    133. 9099 USP2 ubiquitin specific protease 2
    134. 5777 PTPN6 protein tyrosine phosphatase, non-receptor type 6
    135. 59338 PLEKHA1 pleckstrin homology domain containing, family A
    (phosphoinositide binding specific) member 1
    136. 1028 CDKN1C cyclin-dependent kinase inhibitor 1C (p57, Kip2)
  • TABLE IV
    ENTREZ
    GENE ID GENE SYMBOL GENE DESCRIPTION
    1. 6348 CCL3 chemokine (C-C motif) ligand 3
    2. 55388 MCM10 MCM10 minichromosome maintenance deficient 10
    (S. cerevisiae)
    3. 7117 TMSL3 thymosin-like 3
    4. 1017 CDK2 cyclin-dependent kinase 2
    5. 79019 C22orf18 chromosome 22 open reading frame 18
    6. 6241 RRM2 ribonucleotide reductase M2 polypeptide
    7. 4605 MYBL2 v-myb myeloblastosis viral oncogene homolog
    (avian)-like 2
    8. 894 CCND2 cyclin D2
    9. 57405 SPBC25 spindle pole body component 25 homolog (S. cerevisiae)
    10. 146909 LOC146909 hypothetical protein LOC146909
    11. 150271 LOC150271 hypothetical protein LOC150271
    12. 203 AK1 adenylate kinase 1
    13. 4050 LTB lymphotoxin beta (TNF superfamily, member 3)
    14. 257019 FRMD3 FERM domain containing 3
    15. 8357 HIST1H3H histone 1, H3h
    16. 23710 GABARAPL1 GABA(A) receptor-associated protein like 1
    17. 4171 MCM2 MCM2 minichromosome maintenance deficient 2,
    mitotin (S. cerevisiae)
    18. 4176 MCM7 MCM7 minichromosome maintenance deficient 7
    (S. cerevisiae)
    19. 29089 UBE2T ubiquitin-conjugating enzyme E2T (putative)
    20. 890 CCNA2 cyclin A2
    21. 51514 DTL denticleless homolog (Drosophila)
    22. 440279 UNC13C unc-13 homolog C (C. elegans)
    23. 11130 ZWINT ZW10 interactor
    24. 9768 KIAA0101 KIAA0101
    25. 27338 UBE2S ubiquitin-conjugating enzyme E2S
    26. 1846 DUSP4 dual specificity phosphatase 4
    27. 9833 MELK maternal embryonic leucine zipper kinase
    28. 387103 C6orf173 chromosome 6 open reading frame 173
    29. 137392 LOC137392 similar to CG6405 gene product
    30. 7374 UNG uracil-DNA glycosylase
    31. 4915 NTRK2 neurotrophic tyrosine kinase, receptor, type 2
    32. 990 CDC6 CDC6 cell division cycle 6 homolog (S. cerevisiae)
    33. 55165 C10orf3 chromosome 10 open reading frame 3
    34. 4001 LMNB1 lamin B1
    35. 51659 Pfs2 DNA replication complex GINS protein PSF2
    36. 11065 UBE2C ubiquitin-conjugating enzyme E2C
    37. 4174 MCM5 MCM5 minichromosome maintenance deficient 5,
    cell division cycle 46 (S. cerevisiae)
    38. 113130 CDCA5 cell division cycle associated 5
    39. 9535 GMFG glia maturation factor, gamma
    40. 195828 ZNF367 zinc finger protein 367
    41. 55355 DKFZp762E1312 hypothetical protein DKFZp762E1312
    42. 9928 KIF14 kinesin family member 14
    43. 83879 CDCA7 cell division cycle associated 7
    44. 701 BUB1B BUB1 budding uninhibited by benzimidazoles 1
    homolog beta (yeast)
    45. 200734 SPRED2 sprouty-related, EVH1 domain containing 2
    46. 991 CDC20 CDC20 cell division cycle 20 homolog (S. cerevisiae)
    47. 22974 TPX2 TPX2, microtubule-associated protein homolog
    (Xenopus laevis)
    48. 3832 KIF11 kinesin family member 11
    49. 4288 MKI67 antigen identified by monoclonal antibody KI-67
    50. 983 CDC2 cell division cycle 2, G1 to S and G2 to M
    51. 28231 SLCO4A1 solute carrier organic anion transporter family,
    member 4A1
    52. 79801 SHCBP1 SHC SH2-domain binding protein 1
    53. 7804 LRP8 low density lipoprotein receptor-related protein 8,
    apolipoprotein e receptor
    54. 7298 TYMS thymidylate synthetase
    55. 7083 TK1 thymidine kinase 1, soluble
    56. 26147 PHF19 PHD finger protein 19
    57. 55839 BM039 uncharacterized bone marrow protein BM039
    58. 9232 PTTG1 pituitary tumor-transforming 1
    59. 10592 SMC2L1 SMC2 structural maintenance of chromosomes 2-
    like 1 (yeast)
    60. 3398 ID2 inhibitor of DNA binding 2, dominant negative helix-
    loop-helix protein
    61. 4085 MAD2L1 MAD2 mitotic arrest deficient-like 1 (yeast)
    62. 1063 CENPF centromere protein F, 350/400ka (mitosin)
    63. 3418 IDH2 isocitrate dehydrogenase 2 (NADP+), mitochondrial
    64. 1163 CKS1B CDC28 protein kinase regulatory subunit 1B
    65. 55215 FLJ10719 hypothetical protein FLJ10719
    66. 29127 RACGAP1 Rac GTPase activating protein 1
    67. 7153 TOP2A topoisomerase (DNA) II alpha 170 kDa
    68. 122769 PPIL5 peptidylprolyl isomerase (cyclophilin)-like 5
    69. 79682 MLF1IP MLF1 interacting protein
    70. 6790 STK6 serine/threonine kinase 6
    71. 3925 STMN1 stathmin 1/oncoprotein 18
    72. 11004 KIF2C kinesin family member 2C
    73. 10276 NET1 neuroepithelial cell transforming gene 1
    74. 3015 H2AFZ H2A histone family, member Z
    75. 891 CCNB1 cyclin B1
    76. 389835 FAM72A family with sequence similarity 72, member A
    77. 5111 PCNA proliferating cell nuclear antigen
    78. 9837 PSF1 DNA replication complex GINS protein PSF1
    79. 3148 HMGB2 high-mobility group box 2
    80. 7112 TMPO thymopoietin
    81. 63901 FLJ22794 FLJ22794 protein
    82. 51203 NUSAP1 nucleolar and spindle associated protein 1
    83. 29128 UHRF1 ubiquitin-like, containing PHD and RING finger
    domains, 1
    84. 79075 DCC1 defective in sister chromatid cohesion homolog 1 (S. cerevisiae)
    85. 9319 TRIP13 thyroid hormone receptor interactor 13
    86. 1033 CDKN3 cyclin-dependent kinase inhibitor 3 (CDK2-
    associated dual specificity phosphatase)
    87. 10189 THOC4 THO complex 4
    88. 9133 CCNB2 cyclin B2
    89. 55010 FLJ20641 hypothetical protein FLJ20641
    90. 83540 CDCA1 cell division cycle associated 1
    91. 1870 E2F2 E2F transcription factor 2
    92. 962 CD48 CD48 antigen (B-cell membrane protein)
    93. 55789 DEPDC1B DEP domain containing 1B
    94. 170954 KIAA1949 KIAA1949
    95. 332 BIRC5 baculoviral IAP repeat-containing 5 (survivin)
    96. 445815 PALM2-AKAP2 PALM2-AKAP2 protein
    97. 865 CBFB core-binding factor, beta subunit
    98. 7913 DEK DEK oncogene (DNA binding)
    99. 5983 RFC3 replication factor C (activator 1) 3, 38 kDa
    100. 84515 MCM8 MCM8 minichromosome maintenance deficient 8
    (S. cerevisiae)
    101. 51053 GMNN geminin, DNA replication inhibitor
    102. 1111 CHEK1 CHK1 checkpoint homolog (S. pombe)
    103. 7443 VRK1 vaccinia related kinase 1
    104. 10376 K-ALPHA-1 tubulin, alpha, ubiquitous
    105. 3014 H2AFX H2A histone family, member X
    106. 9055 PRC1 protein regulator of cytokinesis 1
    107. 2237 FEN1 flap structure-specific endonuclease 1
    108. 81563 C1orf21 chromosome 1 open reading frame 21
    109. 51192 CKLF chemokine-like factor
    110. 1062 CENPE centromere protein E, 312 kDa
    111. 11339 OIP5 Opa interacting protein 5
    112. 10615 SPAG5 sperm associated antigen 5
    113. 55646 LYAR hypothetical protein FLJ20425
    114. 55706 TMEM48 transmembrane protein 48
    115. 1058 CENPA centromere protein A, 17 kDa
    116. 3070 HELLS helicase, lymphoid-specific
    117. 4173 MCM4 MCM4 minichromosome maintenance deficient 4
    (S. cerevisiae)
    118. 23421 ITGB3BP integrin beta 3 binding protein (beta3-endonexin)
    119. 9530 BAG4 BCL2-associated athanogene 4
    120. 801 CALM1 calmodulin 1 (phosphorylase kinase, delta)
    121. 54069 C21orf45 chromosome 21 open reading frame 45
    122. 283991 MGC29814 hypothetical protein MGC29814
    123. 63979 FIGNL1 fidgetin-like 1
    124. 64105 FKSG14 leucine zipper protein FKSG14
    125. 4172 MCM3 MCM3 minichromosome maintenance deficient 3
    (S. cerevisiae)
    126. 24137 KIF4A kinesin family member 4A
    127. 7398 USP1 ubiquitin specific protease 1
    128. 84930 MASTL microtubule associated serine/threonine kinase-like
    129. 51512 GTSE1 G-2 and S-phase expressed 1
    130. 4678 NASP nuclear autoantigenic sperm protein (histone-
    binding)
    131. 699 BUB1 BUB1 budding uninhibited by benzimidazoles 1
    homolog (yeast)
    132. 1719 DHFR dihydrofolate reductase
    133. 494143 LOC494143 similar to RIKEN cDNA 2510006C20 gene
    134. 55055 FLJ10036 Zwilch
    135. 672 BRCA1 breast cancer 1, early onset
    136. 64946 CENPH centromere protein H
    137. 83461 CDCA3 cell division cycle associated 3
    138. 7465 WEE1 WEE1 homolog (S. pombe)
    139. 5984 RFC4 replication factor C (activator 1) 4, 37 kDa
    140. 64581 CLEC7A C-type lectin domain family 7, member A
    141. 1230 CCR1 chemokine (C-C motif) receptor 1
    142. 4175 MCM6 MCM6 minichromosome maintenance deficient 6
    (MIS5 homolog, S. pombe) (S. cerevisiae)
    143. 55502 HES6 hairy and enhancer of split 6 (Drosophila)
    144. 64151 HCAP-G chromosome condensation protein G
    145. 11151 CORO1A coronin, actin binding protein, 1A
    146. 203068 TUBB tubulin, beta polypeptide
    147. 10926 ASK activator of S phase kinase
    148. 11073 TOPBP1 topoisomerase (DNA) II binding protein 1
    149. 90417 C15orf23 chromosome 15 open reading frame 23
    150. 9493 KIF23 kinesin family member 23
    151. 387882 LOC387882 hypothetical protein
    152. 23234 DNAJC9 DnaJ (Hsp40) homolog, subfamily C, member 9
    153. 2146 EZH2 enhancer of zeste homolog 2 (Drosophila)
    154. 6627 SNRPA1 small nuclear ribonucleoprotein polypeptide A′
    155. 5982 RFC2 replication factor C (activator 1) 2, 40 kDa
    156. 51155 HN1 hematological and neurological expressed 1
    157. 10635 RAD51AP1 RAD51 associated protein 1
    158. 91057 NY-REN-41 NY-REN-41 antigen
    159. 11168 PSIP1 PC4 and SFRS1 interacting protein 1
    160. 10403 KNTC2 kinetochore associated 2
    161. 4751 NEK2 NIMA (never in mitosis gene a)-related kinase 2
    162. 29028 ATAD2 ATPase family, AAA domain containing 2
    163. 26271 FBXO5 F-box protein 5
    164. 54892 LUZP5 leucine zipper protein 5
    165. 79723 SUV39H2 suppressor of variegation 3-9 homolog 2
    (Drosophila)
    166. 23590 TPRT trans-prenyltransferase
    167. 2288 FKBP4 FK506 binding protein 4, 59 kDa
    168. 23165 NUP205 nucleoporin 205 kDa
    169. 6240 RRM1 ribonucleotide reductase M1 polypeptide
    170. 81539 SLC38A1 solute carrier family 38, member 1
    171. 1894 ECT2 epithelial cell transforming sequence 2 oncogene
    172. 55872 PBK PDZ binding kinase
    173. 55635 DEPDC1 DEP domain containing 1
    174. 11013 TMSL8 thymosin-like 8
    175. 259266 ASPM asp (abnormal spindle)-like, microcephaly
    associated (Drosophila)
    176. 10950 BTG3 BTG family, member 3
    177. 56992 KIF15 kinesin family member 15
    178. 29980 DONSON downstream neighbor of SON
    179. 5757 PTMA prothymosin, alpha (gene sequence 28)
    180. 5932 RBBP8 retinoblastoma binding protein 8
    181. 7903 ST8SIA4 ST8 alpha-N-acetyl-neuraminide alpha-2,8-
    sialyltransferase 4
    182. 348235 FAM33A family with sequence similarity 33, member A
    183. 3182 HNRPAB heterogeneous nuclear ribonucleoprotein A/B
    184. 3161 HMMR hyaluronan-mediated motility receptor (RHAMM)
    185. 5985 RFC5 replication factor C (activator 1) 5, 36.5 kDa
    186. 864 RUNX3 runt-related transcription factor 3
    187. 3930 LBR lamin B receptor
    188. 1434 CSE1L CSE1 chromosome segregation 1-like (yeast)
    189. 81610 C20orf129 chromosome 20 open reading frame 129
    190. 3146 HMGB1 high-mobility group box 1
    191. 55636 CHD7 chromodomain helicase DNA binding protein 7
    192. 54443 ANLN anillin, actin binding protein (scraps homolog,
    Drosophila)
    193. 5698 PSMB9 proteasome (prosome, macropain) subunit, beta
    type, 9 (large multifunctional protease 2)
    194. 7277 TUBA1 tubulin, alpha 1 (testis specific)
    195. 64282 PAPD5 PAP associated domain containing 5
    196. 201725 LOC201725 hypothetical protein LOC201725
    197. 7171 TPM4 tropomyosin 4
    198. 3838 KPNA2 karyopherin alpha 2 (RAG cohort 1, importin alpha
    1)
    199. 116832 RPL39L ribosomal protein L39-like
    200. 4602 MYB v-myb myeloblastosis viral oncogene homolog
    (avian)
    201. 54962 FLJ20516 timeless-interacting protein
    202. 10541 ANP32B acidic (leucine-rich) nuclear phosphoprotein 32
    family, member B
    203. 9787 DLG7 discs, large homolog 7 (Drosophila)
    204. 147138 EVER2 epidermodysplasia verruciformis 2
    205. 157313 CDCA2 cell division cycle associated 2
    206. 11340 EXOSC8 exosome component 8
    207. 2956 MSH6 mutS homolog 6 (E. coli)
    208. 151246 SGOL2 shugoshin-like 2 (S. pombe)
    209. 27346 MAC30 hypothetical protein MAC30
    210. 5873 RAB27A RAB27A, member RAS oncogene family
    211. 79596 C13orf7 chromosome 13 open reading frame 7
    212. 10051 SMC4L1 SMC4 structural maintenance of chromosomes 4-
    like 1 (yeast)
    213. 3336 HSPE1 heat shock 10 kDa protein 1 (chaperonin 10)
    214. 6432 SFRS7 splicing factor, arginine/serine-rich 7, 35 kDa
    215. 8819 SAP30 sin3-associated polypeptide, 30 kDa
    216. 54801 FAM29A family with sequence similarity 29, member A
    217. 1123 CHN1 chimerin (chimaerin) 1
    218. 694 BTG1 B-cell translocation gene 1, anti-proliferative
    219. 153222 LOC153222 adult retina protein
    220. 3669 ISG20 interferon stimulated exonuclease gene 20 kDa
    221. 151556 GPR155 G protein-coupled receptor 155
    222. 6591 SNAI2 snail homolog 2 (Drosophila)
    223. 5920 RARRES3 retinoic acid receptor responder (tazarotene
    induced) 3
    224. 400172 LOC400172 similar to KIAA1641 protein; melanoma-associated
    antigen; CLL-associated antigen KW-1
    225. 55281 FLJ11000 hypothetical protein FLJ11000
    226. 9783 RIMS3 regulating synaptic membrane exocytosis 3
    227. 6480 ST6GAL1 ST6 beta-galactosamide alpha-2,6-sialyltranferase 1
    228. 390 RND3 Rho family GTPase 3
    229. 10765 JARID1B Jumonji, AT rich interactive domain 1B (RBP2-like)
    230. 154091 SLC2A12 solute carrier family 2 (facilitated glucose
    transporter), member 12
    231. 54981 C9orf95 chromosome 9 open reading frame 95
    232. 1663 DDX11 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11
    (CHL1-like helicase homolog, S. cerevisiae)
    233. 54800 DRE1 DRE1 protein
    234. 57515 TDE2 tumor differentially expressed 2
    235. 83719 YPEL3 yippee-like 3 (Drosophila)
    236. 5269 SERPINB6 serine (or cysteine) proteinase inhibitor, clade B
    (ovalbumin), member 6
    237. 30061 SLC40A1 solute carrier family 40 (iron-regulated transporter),
    member 1
    238. 5660 PSAP prosaposin (variant Gaucher disease and variant
    metachromatic leukodystrophy)
    239. 51646 YPEL5 yippee-like 5 (Drosophila)
    240. 145788 FLJ27352 hypothetical LOC145788
    241. 81030 ZBP1 Z-DNA binding protein 1
    242. 57035 C1orf63 chromosome 1 open reading frame 63
    243. 9863 MAGI2 membrane associated guanylate kinase, WW and
    PDZ domain containing 2
    244. 9855 FARP2 FERM, RhoGEF and pleckstrin domain protein 2
    245. 57612 KIAA1466 KIAA1466 gene
    246. 56243 KIAA1217 KIAA1217
    247. 8365 HIST1H4H histone 1, H4h
    248. 440081 DDX12 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 12
    (CHL1-like helicase homolog, S. cerevisiae)
    249. 83937 RASSF4 Ras association (RalGDS/AF-6) domain family 4
    250. 56204 FLJ10980 hypothetical protein FLJ10980
    251. 22932 POMZP3 POM (POM121 homolog, rat) and ZP3 fusion
    252. 10628 TXNIP thioredoxin interacting protein
    253. 6720 SREBF1 sterol regulatory element binding transcription factor 1
    254. 1508 CTSB cathepsin B
    255. 84513 HTPAP HTPAP protein
    256. 85352 KIAA1644 KIAA1644 protein
    257. 9388 LIPG lipase, endothelial
    258. 5163 PDK1 pyruvate dehydrogenase kinase, isoenzyme 1
    259. 23446 CDW92 CDW92 antigen
    260. 10156 RASA4 RAS p21 protein activator 4
    261. 23766 GABARAPL3 GABA(A) receptors associated protein like 3
    262. 56904 SH3GLB2 SH3-domain GRB2-like endophilin B2
    263. 6609 SMPD1 sphingomyelin phosphodiesterase 1, acid lysosomal
    (acid sphingomyelinase)
    264. 23259 DDHD2 DDHD domain containing 2
    265. 23092 ARHGAP26 Rho GTPase activating protein 26
    266. 27250 PDCD4 programmed cell death 4 (neoplastic transformation
    inhibitor)
    267. 3983 ABLIM1 actin binding LIM protein 1
    268. 23461 ABCA5 ATP-binding cassette, sub-family A (ABC1),
    member 5
    269. 4094 MAF v-maf musculoaponeurotic fibrosarcoma oncogene
    homolog (avian)
    270. 23646 PLD3 phospholipase D family, member 3
    271. 51566 ARMCX3 armadillo repeat containing, X-linked 3
    272. 58476 TP53INP2 tumor protein p53 inducible nuclear protein 2
    273. 29994 BAZ2B bromodomain adjacent to zinc finger domain, 2B
    274. 283131 TncRNA trophoblast-derived noncoding RNA
    275. 4189 DNAJB9 DnaJ (Hsp40) homolog, subfamily B, member 9
    276. 9123 SLC16A3 solute carrier family 16 (monocarboxylic acid
    transporters), member 3
    277. 8473 OGT O-linked N-acetylglucosamine (GlcNAc) transferase
    (UDP-N-acetylglucosamine:polypeptide-N-
    acetylglucosaminyl transferase)
    278. 65018 PINK1 PTEN induced putative kinase 1
    279. 23512 SUZ12 suppressor of zeste 12 homolog (Drosophila)
    280. 81611 ANP32E acidic (leucine-rich) nuclear phosphoprotein 32
    family, member E
    281. 5880 RAC2 ras-related C3 botulinum toxin substrate 2 (rho
    family, small GTP binding protein Rac2)
    282. 6941 TCF19 transcription factor 19 (SC1)
    283. 8836 GGH gamma-glutamyl hydrolase (conjugase,
    folylpolygammaglutamyl hydrolase)
    284. 9830 TRIM14 tripartite motif-containing 14
    285. 55026 FLJ20716 hypothetical protein FLJ20716
    286. 84057 GAJ GAJ protein
    287. 6510 SLC1A5 solute carrier family 1 (neutral amino acid
    transporter), member 5
    288. 84969 C20orf100 chromosome 20 open reading frame 100
    289. 81620 CDT1 DNA replication factor
    290. 113115 FAM54A family with sequence similarity 54, member A
    291. 3159 HMGA1 high mobility group AT-hook 1
    292. 3251 HPRT1 hypoxanthine phosphoribosyltransferase 1 (Lesch-
    Nyhan syndrome)
    293. 5214 PFKP phosphofructokinase, platelet
    294. 2171 FABP5 fatty acid binding protein 5 (psoriasis-associated)
    295. 57082 CASC5 cancer susceptibility candidate 5
    296. 5889 RAD51C RAD51 homolog C (S. cerevisiae)
    297. 6628 SNRPB small nuclear ribonucleoprotein polypeptides B and
    B1
    298. 134111 FLJ25076 similar to CG4502-PA
    299. 397 ARHGDIB Rho GDP dissociation inhibitor (GDI) beta
    300. 129401 NUP35 nucleoporin 35 kDa
    301. 6632 SNRPD1 small nuclear ribonucleoprotein D1 polypeptide
    16 kDa
    302. 10212 DDX39 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39
    303. 6472 SHMT2 serine hydroxymethyltransferase 2 (mitochondrial)
    304. 55536 CDCA7L cell division cycle associated 7-like
    305. 64116 SLC39A8 solute carrier family 39 (zinc transporter), member 8
    306. 79902 PCNT1 pericentrin 1
    307. 7371 UCK2 uridine-cytidine kinase 2
    308. 11332 BACH brain acyl-CoA hydrolase
    309. 3320 HSPCA heat shock 90 kDa protein 1, alpha
    310. 1019 CDK4 cyclin-dependent kinase 4
    311. 10383 TUBB2 tubulin, beta, 2
    312. 8243 SMC1L1 SMC1 structural maintenance of chromosomes 1-
    like 1 (yeast)
    313. 1786 DNMT1 DNA (cytosine-5-)-methyltransferase 1
    314. 22929 SEPHS1 selenophosphate synthetase 1
    315. 10492 SYNCRIP synaptotagm in binding, cytoplasmic RNA interacting
    protein
    316. 26051 PPP1R16B protein phosphatase 1, regulatory (inhibitor) subunit
    16B
    317. 5168 ENPP2 ectonucleotide pyrophosphatase/phosphodiesterase
    2 (autotaxin)
    318. 51144 HSD17B12 hydroxysteroid (17-beta) dehydrogenase 12
    319. 9446 GSTO1 glutathione S-transferase omega 1
    320. 51002 CGI-121 CGI-121 protein
    321. 51377 UCHL5 ubiquitin carboxyl-terminal hydrolase L5
    322. 10606 PAICS phosphoribosylaminoimidazole carboxylase,
    phosphoribosylaminoimidazole succinocarboxamide
    synthetase
    323. 6929 TCF3 transcription factor 3 (E2A immunoglobulin
    enhancer binding factors E12/E47)
    324. 262 AMD1 adenosylmethionine decarboxylase 1
    325. 3676 ITGA4 integrin, alpha 4 (antigen CD49D, alpha 4 subunit of
    VLA-4 receptor)
    326. 39 ACAT2 acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl
    Coenzyme A thiolase)
    327. 23526 HA-1 minor histocompatibility antigen HA-1
    328. 79023 NUP37 nucleoporin 37 kDa
    329. 6119 RPA3 replication protein A3, 14 kDa
    330. 6657 SOX2 SRY (sex determining region Y)-box 2
    331. 27101 CACYBP calcyclin binding protein
    332. 55752 11-Sep septin 11
    333. 79017 C7orf24 chromosome 7 open reading frame 24
    334. 10808 HSPH1 heat shock 105 kDa/110 kDa protein 1
    335. 11051 NUDT21 nudix (nucleoside diphosphate linked moiety X)-type
    motif 21
    336. 5631 PRPS1 phosphoribosyl pyrophosphate synthetase 1
    337. 55352 HSA272196 hypothetical protein, clone 2746033
    338. 8727 CTNNAL1 catenin (cadherin-associated protein), alpha-like 1
    339. 26586 CKAP2 cytoskeleton associated protein 2
    340. 2271 FH fumarate hydratase
    341. 23246 BOP1 block of proliferation 1
    342. 5696 PSMB8 proteasome (prosome, macropain) subunit, beta
    type, 8 (large multifunctional protease 7)
    343. 25804 LSM4 LSM4 homolog, U6 small nuclear RNA associated
    (S. cerevisiae)
    344. 5557 PRIM1 primase, polypeptide 1, 49 kDa
    345. 4436 MSH2 mutS homolog 2, colon cancer, nonpolyposis type 1
    (E. coli)
    346. 5885 RAD21 RAD21 homolog (S. pombe)
    347. 22948 CCT5 chaperonin containing TCP1, subunit 5 (epsilon)
    348. 9126 CSPG6 chondroitin sulfate proteoglycan 6 (bamacan)
    349. 9184 BUB3 BUB3 budding uninhibited by benzimidazoles 3
    homolog (yeast)
    350. 4869 NPM1 nucleophosmin (nucleolar phosphoprotein B23,
    numatrin)
    351. 3150 HMGN1 high-mobility group nucleosome binding domain 1
    352. 10409 BASP1 brain abundant, membrane attached signal protein 1
    353. 4200 ME2 malic enzyme 2, NAD(+)-dependent, mitochondrial
    354. 169270 ZNF596 zinc finger protein 596
    355. 3939 LDHA lactate dehydrogenase A
    356. 961 CD47 CD47 antigen (Rh-related antigen, integrin-
    associated signal transducer)
    357. 9368 SLC9A3R1 solute carrier family 9 (sodium/hydrogen
    exchanger), isoform 3 regulator 1
    358. 7086 TKT transketolase (Wernicke-Korsakoff syndrome)
    359. 10801 9-Sep septin 9
    360. 10785 WDR4 WD repeat domain 4
    361. 3033 HADHSC L-3-hydroxyacyl-Coenzyme A dehydrogenase, short
    chain
    362. 8833 GMPS guanine monphosphate synthetase
    363. 27316 RBMX RNA binding motif protein, X-linked
    364. 5725 PTBP1 polypyrimidine tract binding protein 1
    365. 10128 LRPPRC leucine-rich PPR-motif containing
    366. 84250 ANKRD32 ankyrin repeat domain 32
    367. 5358 PLS3 plastin 3 (T isoform)
    368. 4673 NAP1L1 nucleosome assembly protein 1-like 1
    369. 3149 HMGB3 high-mobility group box 3
    370. 2289 FKBP5 FK506 binding protein 5
    371. 22856 CHSY1 carbohydrate (chondroitin) synthase 1
    372. 6566 SLC16A1 solute carrier family 16 (monocarboxylic acid
    transporters), member 1
    373. 54149 C21orf91 chromosome 21 open reading frame 91
    374. 54517 FLJ20485 hypothetical protein FLJ20485
    375. 8514 KCNAB2 potassium voltage-gated channel, shaker-related
    subfamily, beta member 2
    376. 119 ADD2 adducin 2 (beta)
    377. 1407 CRY1 cryptochrome 1 (photolyase-like)
    378. 204 AK2 adenylate kinase 2
    379. 467 ATF3 activating transcription factor 3
    380. 64778 FNDC3B fibronectin type III domain containing 3B
    381. 347733 RP11-506K6.1 tubulin, beta polypeptide paralog
    382. 9604 RNF14 ring finger protein 14
    383. 7832 BTG2 BTG family, member 2
    384. 120196 MGC34830 hypothetical protein MGC34830
    385. 9910 RABGAP1L RAB GTPase activating protein 1-like
    386. 55876 GSDML gasdermin-like
    387. 1524 CX3CR1 chemokine (C—X3—C motif) receptor 1
    388. 23015 GM88 88-kDa golgi protein
    389. 1604 DAF decay accelerating factor for complement (CD55,
    Cromer blood group system)
    390. 114793 FMNL2 formin-like 2
    391. 50640 IPLA2(GAMMA) intracellular membrane-associated calcium-
    independent phospholipase A2 gamma
    392. 222166 Ells1 hypothetical protein Ells1
    393. 10140 TOB1 transducer of ERBB2, 1
    394. 1647 GADD45A growth arrest and DNA-damage-inducible, alpha
    395. 25840 DKFZP586A0522 DKFZP586A0522 protein
    396. 150759 LOC150759 hypothetical protein LOC150759
    397. 6448 SGSH N-sulfoglucosamine sulfohydrolase (sulfamidase)
    398. 85236 HIST1H2BK histone 1, H2bk
    399. 9728 KIAA0256 KIAA0256 gene product
    400. 3727 JUND jun D proto-oncogene
    401. 54741 LEPROT leptin receptor overlapping transcript
    402. 5973 RENBP renin binding protein
    403. 84897 TBRG1 transforming growth factor beta regulator 1
    404. 92370 ACPL2 acid phosphatase-like 2
    405. 23208 SYT11 synaptotagmin XI
    406. 375593 TRIM50B tripartite motif-containing 50B
    407. 94241 TP53INP1 tumor protein p53 inducible nuclear protein 1
    408. 1612 DAPK1 death-associated protein kinase 1
    409. 144203 OVOS2 ovostatin 2
    410. 3915 LAMC1 laminin, gamma 1 (formerly LAMB2)
    411. 115701 ALPK2 alpha-kinase 2
    412. 1203 CLN5 ceroid-lipofuscinosis, neuronal 5
    413. 51363 GALNAC4S-6ST B cell RAG associated protein
    414. 387263 C6orf120 chromosome 6 open reading frame 120
    415. 2824 GPM6B glycoprotein M6B
    416. 8516 ITGA8 integrin, alpha 8
    417. 57730 KIAA1641 KIAA1641
    418. 10370 CITED2 Cbp/p300-interacting transactivator, with Glu/Asp-
    rich carboxy-terminal domain, 2
    419. 1611 DAP death-associated protein
    420. 388677 NOTCH2NL Notch homolog 2 (Drosophila) N-terminal like
    421. 132720 FLJ39370 hypothetical protein FLJ39370
    422. 29005 PRO1073 PRO1073 protein
    423. 1030 CDKN2B cyclin-dependent kinase inhibitor 2B (p15, inhibits
    CDK4)
    424. 23336 DMN desmuslin
    425. 23643 LY96 lymphocyte antigen 96
    426. 4779 NFE2L1 nuclear factor (erythroid-derived 2)-like 1
    427. 7286 TUFT1 tuftelin 1
    428. 1200 TPP1 tripeptidyl peptidase I
    429. 27344 PCSK1N proprotein convertase subtilisin/kexin type 1 inhibitor
    430. 9473 C1orf38 chromosome 1 open reading frame 38
    431. 401152 LOC401152 HCV F-transactivated protein 1
    432. 5360 PLTP phospholipid transfer protein
    433. 7846 TUBA3 tubulin, alpha 3
    434. 9240 PNMA1 paraneoplastic antigen MA1
    435. 81631 MAP1LC3B microtubule-associated protein 1 light chain 3 beta
    436. 112770 C1orf85 chromosome 1 open reading frame 85
    437. 3998 LMAN1 lectin, mannose-binding, 1
    438. 8987 GENX-3414 genethonin 1
    439. 84218 TBC1D3 TBC1 domain family, member 3
    440. 51237 PACAP proapoptotic caspase adaptor protein
    441. 55818 JMJD1A jumonji domain containing 1A
    442. 11057 ABHD2 abhydrolase domain containing 2
    443. 2180 ACSL1 acyl-CoA synthetase long-chain family member 1
    444. 10525 HYOU1 hypoxia up-regulated 1
    445. 114915 TIGA1 TIGA1
    446. 55251 C20orf36 chromosome 20 open reading frame 36
    447. 598 BCL2L1 BCL2-like 1
    448. 51111 SUV420H1 suppressor of variegation 4-20 homolog 1
    (Drosophila)
    449. 64065 PERP PERP, TP53 apoptosis effector
    450. 2037 EPB41L2 erythrocyte membrane protein band 4.1-like 2
    451. 89796 NAV1 neuron navigator 1
    452. 9341 VAMP3 vesicle-associated membrane protein 3 (cellubrevin)
    453. 1465 CSRP1 cysteine and glycine-rich protein 1
    454. 60492 MDS025 hypothetical protein MDS025
    455. 339448 LOC339448 hypothetical protein LOC339448
    456. 6513 SLC2A1 solute carrier family 2 (facilitated glucose
    transporter), member 1
    457. 3995 FADS3 fatty acid desaturase 3
    458. 155038 GIMAP8 GTPase, IMAP family member 8
    459. 90634 CG018 hypothetical gene CG018
    460. 55573 H41 hypothetical protein H41
    461. 7514 XPO1 exportin 1 (CRM1 homolog, yeast)
    462. 196527 TMEM16F transmembrane protein 16F
    463. 5471 PPAT phosphoribosyl pyrophosphate amidotransferase
    464. 22823 MTF2 metal response element binding transcription factor 2
    465. 10856 RUVBL2 RuvB-like 2 (E. coli)
    466. 6713 SQLE squalene epoxidase
    467. 8407 TAGLN2 transgelin 2
    468. 26135 PAI-RBP1 PAI-1 mRNA binding protein
    469. 84247 LDOC1L leucine zipper, down-regulated in cancer 1-like
    470. 9201 DCAMKL1 doublecortin and CaM kinase-like 1
    471. 388403 YPEL2 yippee-like 2 (Drosophila)
    472. 255631 COL24A1 collagen, type XXIV, alpha 1
    473. 8440 NCK2 NCK adaptor protein 2
    474. 81790 RNF170 ring finger protein 170
    475. 9706 ULK2 unc-51-like kinase 2 (C. elegans)
    476. 4092 SMAD7 SMAD, mothers against DPP homolog 7
    (Drosophila)
    477. 51184 MGC14560 protein x 0004
    478. 7334 UBE2N ubiquitin-conjugating enzyme E2N (UBC13
    homolog, yeast)
    479. 84955 NUDCD1 NudC domain containing 1
    480. 5684 PSMA3 proteasome (prosome, macropain) subunit, alpha
    type, 3
    481. 51465 UBE2J1 ubiquitin-conjugating enzyme E2, J1 (UBC6
    homolog, yeast)
    482. 286319 TUSC1 tumor suppressor candidate 1
    483. 26207 PITPNC1 phosphatidylinositol transfer protein, cytoplasmic 1
    484. 51303 FKBP11 FK506 binding protein 11, 19 kDa
    485. 9139 CBFA2T2 core-binding factor, runt domain, alpha subunit 2;
    translocated to, 2
    486. 57714 KIAA1618 KIAA1618
    487. 94240 EPSTI1 epithelial stromal interaction 1 (breast)
    488. 659 BMPR2 bone morphogenetic protein receptor, type II
    (serine/threonine kinase)
    489. 934 CD24 CD24 antigen (small cell lung carcinoma cluster 4
    antigen)
    490. 9532 BAG2 BCL2-associated anthanogene 2
    491. 23331 KIAA1043 KIAA1043 protein
    492. 10675 CSPG5 chondroitin sulfate proteoglycan 5 (neuroglycan C)
    493. 1102 RCBTB2 regulator of chromosome condensation (RCC1) and
    BTB (POZ) domain containing protein 2
    494. 2119 ETV5 ets variant gene 5 (ets-related molecule)
    495. 255488 IBRDC2 IBR domain containing 2
    496. 55076 TMEM45A transmembrane protein 45A
    497. 8364 HIST1H4C histone 1, H4c
    498. 3725 JUN v-jun sarcoma virus 17 oncogene homolog (avian)
    499. 384 ARG2 arginase, type II
    500. 10129 13CDNA73 hypothetical protein CG003
    501. 1960 EGR3 early growth response 3
    502. 27122 DKK3 dickkopf homolog 3 (Xenopus laevis)
    503. 11178 LZTS1 leucine zipper, putative tumor suppressor 1
    504. 143888 KDELC2 KDEL (Lys-Asp-Glu-Leu) containing 2
    505. 1601 DAB2 disabled homolog 2, mitogen-responsive
    phosphoprotein (Drosophila)
    506. 6542 SLC7A2 solute carrier family 7 (cationic amino acid
    transporter, y+ system), member 2
    507. 477 ATP1A2 ATPase, Na+/K+ transporting, alpha 2 (+)
    polypeptide
    508. 90161 HS6ST2 heparan sulfate 6-O-sulfotransferase 2
    509. 81031 SLC2A10 solute carrier family 2 (facilitated glucose
    transporter), member 10
    510. 56675 NRIP3 nuclear receptor interacting protein 3
    511. 1958 EGR1 early growth response 1
    512. 3714 JAG2 jagged 2
    513. 3897 L1CAM L1 cell adhesion molecule
    514. 1488 CTBP2 C-terminal binding protein 2
    515. 145173 B3GTL beta 3-glycosyltransferase-like
    516. 112399 EGLN3 egl nine homolog 3 (C. elegans)
    517. 22871 NLGN1 neuroligin 1
    518. 8804 CREG1 cellular repressor of E1A-stimulated genes 1
    519. 401081 FLJ22763 hypothetical gene supported by AK026416
    520. 25924 MYRIP myosin VIIA and Rab interacting protein
    521. 91694 FLJ23749 hypothetical protein FLJ23749
    522. 56155 TEX14 testis expressed sequence 14
    523. 1349 COX7B cytochrome c oxidase subunit VIIb
    524. 3695 ITGB7 integrin, beta 7
    525. 1164 CKS2 CDC28 protein kinase regulatory subunit 2
    526. 56919 DHX33 DEAH (Asp-Glu-Ala-His) box polypeptide 33
    527. 3276 HRMT1L2 HMT1 hnRNP methyltransferase-like 2 (S. cerevisiae)
    528. 116151 C20orf108 chromosome 20 open reading frame 108
    529. 25758 G2 G2 protein
    530. 25861 DFNB31 deafness, autosomal recessive 31
    531. 9666 DZIP3 zinc finger DAZ interacting protein 3
    532. 1486 CTBS chitobiase, di-N-acetyl-
    533. 3123 HLA-DRB1 major histocompatibility complex, class II, DR beta 1
    534. 317649 EIF4E3 eukaryotic translation initiation factor 4E member
    535. 50854 C6orf48 chromosome 6 open reading frame 48
    536. 401024 FLJ44048 FLJ44048 protein
    537. 114327 EFHC1 EF-hand domain (C-terminal) containing 1
    538. 8334 HIST1H2AC histone 1, H2ac
    539. 284214 LOC284214 hypothetical protein LOC284214
    540. 10379 ISGF3G interferon-stimulated transcription factor 3, gamma
    48 kDa
    541. 113177 C19orf36 chromosome 19 open reading frame 36
    542. 56951 C5orf15 chromosome 5 open reading frame 15
    543. 285362 SUMF1 sulfatase modifying factor 1
    544. 3490 IGFBP7 insulin-like growth factor binding protein 7
    545. 1186 CLCN7 chloride channel 7
    546. 582 BBS1 Bardet-Biedl syndrome 1
    547. 339456 LOC339456 hypothetical protein LOC339456
    548. 26115 DKFZP564D166 putative ankyrin-repeat containing protein
    549. 9895 KIAA0329 KIAA0329
    550. 1040 CDS1 CDP-diacylglycerol synthase (phosphatidate
    cytidylyltransferase) 1
    551. 51496 HSPC129 hypothetical protein HSPC129
    552. 1039 CDR2 cerebellar degeneration-related protein 2, 62 kDa
    553. 130589 GALM galactose mutarotase (aldose 1-epimerase)
    554. 3937 LCP2 lymphocyte cytosolic protein 2 (SH2 domain
    containing leukocyte protein of 76 kDa)
    555. 3535 IGL@ immunoglobulin lambda locus
    556. 1396 CRIP1 cysteine-rich protein 1 (intestinal)
    557. 4291 MLF1 myeloid leukemia factor 1
    558. 9972 NUP153 nucleoporin 153 kDa
    559. 10459 MAD2L2 MAD2 mitotic arrest deficient-like 2 (yeast)
    560. 483 ATP1B3 ATPase, Na+/K+ transporting, beta 3 polypeptide
    561. 8165 AKAP1 A kinase (PRKA) anchor protein 1
    562. 29097 CNIH4 cornichon homolog 4 (Drosophila)
    563. 7037 TFRC transferrin receptor (p90, CD71)
    564. 509 ATP5C1 ATP synthase, H+ transporting, mitochondrial F1
    complex, gamma polypeptide 1
    565. 10682 EBP emopamil binding protein (sterol isomerase)
    566. 56172 ANKH ankylosis, progressive homolog (mouse)
    567. 100 ADA adenosine deaminase
    568. 2821 GPI glucose phosphate isomerase
    569. 54927 CHCHD3 coiled-coil-helix-coiled-coil-helix domain containing 3
    570. 58478 MASA E-1 enzyme
    571. 292 SLC25A5 solute carrier family 25 (mitochondrial carrier;
    adenine nucleotide translocator), member 5
    572. 51096 WDR50 WD repeat domain 50
    573. 79053 ALG8 asparagine-linked glycosylation 8 homolog (yeast,
    alpha-1,3-glucosyltransferase)
    574. 84300 C6orf125 chromosome 6 open reading frame 125
    575. 253461 ZBTB38 zinc finger and BTB domain containing 38
    576. 29080 HSPC128 HSPC128 protein
    577. 1622 DBI diazepam binding inhibitor (GABA receptor
    modulator, acyl-Coenzyme A binding protein)
    578. 2029 ENSA endosulfine alpha
    579. 6404 SELPLG selectin P ligand
    580. 7295 TXN thioredoxin
    581. 10539 TXNL2 thioredoxin-like 2
    582. 3422 IDI1 isopentenyl-diphosphate delta isomerase
    583. 1964 EIF1AX eukaryotic translation initiation factor 1A, X-linked
    584. 11191 PTENP1 phosphatase and tensin homolog (mutated in
    multiple advanced cancers 1), pseudogene 1
    585. 80853 KIAA1718 KIAA1718 protein
    586. 7096 TLR1 toll-like receptor 1
    587. 440270 LOC440270 golgin-67
    588. 8879 SGPL1 sphingosine-1-phosphate lyase 1
    589. 493812 HCG11 HLA complex group 11
    590. 257103 C21orf86 chromosome 21 open reading frame 86
    591. 55615 PRR5 proline rich protein 5
    592. 7905 C5orf18 chromosome 5 open reading frame 18
    593. 64062 C13orf10 chromosome 13 open reading frame 10
    594. 10133 OPTN optineurin
    595. 10116 FEM1B fem-1 homolog b (C. elegans)
    596. 79027 ZNF655 zinc finger protein 655
    597. 79717 FLJ11838 hypothetical protein FLJ11838
    598. 10397 NDRG1 N-myc downstream regulated gene 1
    599. 3338 DNAJC4 DnaJ (Hsp40) homolog, subfamily C, member 4
  • TABLE V
    ENTREZ
    GENE ID GENE SYMBOL GENE DESCRIPTION
    1. 934 CD24 CD24 antigen (small cell lung carcinoma cluster 4
    antigen)
    2. 9532 BAG2 BCL2-associated athanogene 2
    3. 23331 KIAA1043 KIAA1043 protein
    4. 10675 CSPG5 chondroitin sulfate proteoglycan 5 (neuroglycan C)
    5. 1102 RCBTB2 regulator of chromosome condensation (RCC1) and
    BTB (POZ) domain containing protein 2
    6. 2119 ETV5 ets variant gene 5 (ets-related molecule)
    7. 255488 IBRDC2 IBR domain containing 2
    8. 55076 TMEM45A transmembrane protein 45A
    9. 8364 HIST1H4C histone 1, H4c
    10. 3725 JUN v-jun sarcoma virus 17 oncogene homolog (avian)
    11. 384 ARG2 arginase, type II
    12. 10129 13CDNA73 hypothetical protein CG003
    13. 401081 FLJ22763 hypothetical gene supported by AK026416
    14. 25924 MYRIP myosin VIIA and Rab interacting protein
    15. 91694 FLJ23749 hypothetical protein FLJ23749
    16. 56155 TEX14 testis expressed sequence 14
    17. 1349 COX7B cytochrome c oxidase subunit VIIb
    18. 1164 CKS2 CDC28 protein kinase regulatory subunit 2
    19. 56919 DHX33 DEAH (Asp-Glu-Ala-His) box polypeptide 33
    20. 3276 HRMT1L2 HMT1 hnRNP methyltransferase-like 2 (S. cerevisiae)
    21. 3695 ITGB7 integrin, beta 7
    22. 51496 HSPC129 hypothetical protein HSPC129
    23. 1039 CDR2 cerebellar degeneration-related protein 2, 62 kDa
    24. 130589 GALM galactose mutarotase (aldose 1-epimerase)
    25. 3937 LCP2 lymphocyte cytosolic protein 2 (SH2 domain
    containing leukocyte protein of 76 kDa)
    26. 3535 IGL@ immunoglobulin lambda locus
    27. 1396 CRIP1 cysteine-rich protein 1 (intestinal)
    28. 4291 MLF1 myeloid leukemia factor 1
    29. 9972 NUP153 nucleoporin 153 kDa
    30. 10459 MAD2L2 MAD2 mitotic arrest deficient-like 2 (yeast)
    31. 483 ATP1B3 ATPase, Na+/K+ transporting, beta 3 polypeptide
    32. 8165 AKAP1 A kinase (PRKA) anchor protein 1
    33. 29097 CNIH4 cornichon homolog 4 (Drosophila)
    34. 7037 TFRC transferrin receptor (p90, CD71)
    35. 509 ATP5C1 ATP synthase, H+ transporting, mitochondrial F1
    complex, gamma polypeptide 1
    36. 10682 EBP emopamil binding protein (sterol isomerase)
    37. 56172 ANKH ankylosis, progressive homolog (mouse)
    38. 100 ADA adenosine deaminase
    39. 2821 GPI glucose phosphate isomerase
    40. 54927 CHCHD3 coiled-coil-helix-coiled-coil-helix domain containing 3
    41. 58478 MASA E-1 enzyme
    42. 292 SLC25A5 solute carrier family 25 (mitochondrial carrier;
    adenine nucleotide translocator), member 5
    43. 51096 WDR50 WD repeat domain 50
    44. 79053 ALG8 asparagine-linked glycosylation 8 homolog (yeast,
    alpha-1,3-glucosyltransferase)
    45. 84300 C6orf125 chromosome 6 open reading frame 125
    46. 253461 ZBTB38 zinc finger and BTB domain containing 38
    47. 29080 HSPC128 HSPC128 protein
    48. 1622 DBI diazepam binding inhibitor (GABA receptor
    modulator, acyl-Coenzyme A binding protein)
    49. 2029 ENSA endosulfine alpha
    50. 6404 SELPLG selectin P ligand
    51. 7295 TXN thioredoxin
    52. 10539 TXNL2 thioredoxin-like 2
    53. 3422 IDI1 isopentenyl-diphosphate delta isomerase
    54. 1964 EIF1AX eukaryotic translation initiation factor 1A, X-linked
    55. 11191 PTENP1 phosphatase and tensin homolog (mutated in
    multiple advanced cancers 1), pseudogene 1
    56. 1960 EGR3 early growth response 3
    57. 3338 DNAJC4 DnaJ (Hsp40) homolog, subfamily C, member 4
    58. 10397 NDRG1 N-myc downstream regulated gene 1
    59. 79717 FLJ11838 hypothetical protein FLJ11838
    60. 79027 ZNF655 zinc finger protein 655
    61. 10116 FEM1B fem-1 homolog b (C. elegans)
    62. 10133 OPTN optineurin
    63. 64062 C13orf10 chromosome 13 open reading frame 10
    64. 7905 C5orf18 chromosome 5 open reading frame 18
    65. 55615 PRR5 proline rich protein 5
    66. 257103 C21orf86 chromosome 21 open reading frame 86
    67. 493812 HCG11 HLA complex group 11
    68. 8879 SGPL1 sphingosine-1-phosphate lyase 1
    69. 440270 LOC440270 golgin-67
    70. 7096 TLR1 toll-like receptor 1
    71. 80853 KIAA1718 KIAA1718 protein
    72. 1040 CDS1 CDP-diacylglycerol synthase (phosphatidate
    cytidylyltransferase) 1
    73. 9895 KIAA0329 KIAA0329
    74. 26115 DKFZP564D166 putative ankyrin-repeat containing protein
    75. 339456 LOC339456 hypothetical protein LOC339456
    76. 582 BBS1 Bardet-Biedl syndrome 1
    77. 1186 CLCN7 chloride channel 7
    78. 3490 IGFBP7 insulin-like growth factor binding protein 7
    79. 285362 SUMF1 sulfatase modifying factor 1
    80. 56951 C5orf15 chromosome 5 open reading frame 15
    81. 113177 C19orf36 chromosome 19 open reading frame 36
    82. 10379 ISGF3G interferon-stimulated transcription factor 3, gamma
    48 kDa
    83. 284214 LOC284214 hypothetical protein LOC284214
    84. 8334 HIST1H2AC histone 1, H2ac
    85. 114327 EFHC1 EF-hand domain (C-terminal) containing 1
    86. 401024 FLJ44048 FLJ44048 protein
    87. 50854 C6orf48 chromosome 6 open reading frame 48
    88. 317649 EIF4E3 eukaryotic translation initiation factor 4E member 3
    89. 3123 HLA-DRB1 major histocompatibility complex, class II, DR beta 1
    90. 1486 CTBS chitobiase, di-N-acetyl-
    91. 9666 DZIP3 zinc finger DAZ interacting protein 3
    92. 25861 DFNB31 deafness, autosomal recessive 31
    93. 25758 G2 G2 protein
    94. 116151 C20orf108 chromosome 20 open reading frame 108
    95. 8804 CREG1 cellular repressor of E1A-stimulated genes 1
    96. 22871 NLGN1 neuroligin 1
    97. 112399 EGLN3 egl nine homolog 3 (C. elegans)
    98. 145173 B3GTL beta 3-glycosyltransferase-like
    99. 1488 CTBP2 C-terminal binding protein 2
    100. 3897 L1CAM L1 cell adhesion molecule
    101. 3714 JAG2 jagged 2
    102. 1958 EGR1 early growth response 1
    103. 56675 NRIP3 nuclear receptor interacting protein 3
    104. 81031 SLC2A10 solute carrier family 2 (facilitated glucose
    transporter), member 10
    105. 90161 HS6ST2 heparan sulfate 6-O-sulfotransferase 2
    106. 477 ATP1A2 ATPase, Na+/K+ transporting, alpha 2 (+)
    polypeptide
    107. 6542 SLC7A2 solute carrier family 7 (cationic amino acid
    transporter, y+ system), member 2
    108. 1601 DAB2 disabled homolog 2, mitogen-responsive
    phosphoprotein (Drosophila)
    109. 143888 KDELC2 KDEL (Lys-Asp-Glu-Leu) containing 2
    110. 11178 LZTS1 leucine zipper, putative tumor suppressor 1
    111. 27122 DKK3 dickkopf homolog 3 (Xenopus laevis)
  • The gene expression of the biomarkers of Table I or any of its subsets, Tables II through V, may be up- or down-regulated in response to the inhibition of FGFR3. In some instances, the detection of the presence of gene expression of one of the biomarkers may be sufficient to identify the patient for treatment or provide indication of a favorable response to treatment. In other instances, one may prefer the guidance provided by a higher level of alteration of gene expression or a stronger correlation with a particular inhibitory compound.
  • Further, in some instances, one may find identifying the most suitable patients for treatment for a particular cell proliferative disorder may best be accomplished by detecting an alteration in level of gene expression of two or more biomarkers or by a specific combination of biomarkers or even direction of alteration of gene expression. For example, a particular two of the biomarkers identified in Table I may be most correlated with a given condition and, thus, guide a certain treatment. Alternatively, a ratio of the relative levels of gene expression of two particular biomarkers may be indicative of the suitability of a given treatment for a patient. It is also contemplated that a particular condition may have a signature such as the up-regulation of one or more particular biomarker or biomarkers and/or the down-regulation of one or more other particular biomarker or biomarkers.
  • The alteration in the level of gene expression may be compared to a baseline level. A baseline level may be established in several ways. For example, in a method of monitoring response of a patient to treatment, a sample may be obtained from the patient and tested for measurement of gene expression prior to introduction of an FGFR3 inhibitor to the patient. Thus, the profile of gene expression levels, if any, of biomarkers in a treatment-naïve individual may serve as a baseline for that individual and later tests performed on samples obtained once treatment has begun may be compared to the individual's baseline. Alternatively, a baseline may be established through creation of a guide that consolidates information on gene expression levels taken from a pool of healthy or treatment-naïve individuals or even from an appropriate cell culture. Further, information on baseline levels of gene expression of particular biomarkers may be gathered from published sources or a gene database.
  • In one aspect, a sample is isolated from the patient after receipt of an amount of inhibitor of FGFR3, whether a therapeutically effective amount or a sub-therapeutically effective amount, which may be adequate for some purposes. Cell or tissue samples used for this invention encompass body fluid, solid tissue samples, tissue cultures or cells derived therefrom and the progeny thereof, and sections or smears prepared from any of these sources, or any other samples that may contain genetic information. Measurement of the expression of the biomarkers is described in further detail below.
    • Inhibitors of FGFR3
  • Some examples of small molecule inhibitors of FGFR3 include CHIR-258 (Chiron Corporation), SU-5402 (Pfizer, Inc.), and PD-173074 (Pfizer, Inc.).
  • The chemical structure and chemical name of CHIR-258 are shown below.
  • Figure US20120149714A1-20120614-C00001
  • 4-Amino-5-fluoro-3-[6-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]quinolin-2(1H)-one is a small molecule inhibitor of VEGF-RTK, PDGF-RTK and other receptor tyrosine kinases such as fibroblast growth factor receptor (FGF-RTK). This compound has been described in a patent and several patent applications, the entire disclosures of which are incorporated herein by reference and for all purposes: U.S. Pat. No. 6,605,617, U.S. Ser. No. 10/644,055, U.S. Provisional Application Nos. 60/405,729, 60/428,210, and 60/484,048.
  • Related compounds are disclosed in patents and applications incorporated herein by reference, as noted. A plethora of substituted quinolinone compounds including quinolinone benzimidazolyl compounds and 4-amino substituted quinolinone benzimidazolyl compounds such as 4-amino-5-fluoro-3-[5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]quinolin-2(1H)-one have recently been disclosed in references such as WO 02/22598, WO 2004/043389, WO 2005/047244, U.S. 2004/0220196, U.S. 2005/0137399, WO 2005/046590, and WO 2005/046589. Such compounds are disclosed as inhibiting VEGF-RTKs. Such compounds are also disclosed in published. United States patent applications U.S. 2002/0107392 and U.S. 2003/0028018 and U.S. Pat. Nos. 6,605,617, 6,774,237, 6,762,194, and 6,800,760. Other such compounds are disclosed along with new uses of such compounds in inhibiting serine/threonine kinases and tyrosine kinases are disclosed in WO 2004/018419, and U.S. 2004/0092535, filed on Aug. 19, 2003, and claiming priority to each of the following provisional applications: U.S. Provisional Application No. 60/405,729 filed on Aug. 23, 2002; U.S. Provisional Application No. 60/426,107 filed on Nov. 13, 2002; U.S. Provisional Application No. 60/426,226 filed on Nov. 13, 2002; U.S. Provisional Application No. 60/426,282 filed on Nov. 13, 2002; U.S. Provisional Application No. 60/428,210 filed on Nov. 21, 2002; U.S. Provisional Application No. 60/460,327 filed on Apr. 3, 2003; U.S. Provisional Application Ser. No. ______ filed on Apr. 3, 2003; U.S. Provisional Application No. 60/460,493 filed on Apr. 3, 2003; U.S. Provisional Application No. 60/478,916 filed on Jun. 16, 2003; and U.S. Provisional Application No. 60/484,048 filed on Jul. 1, 2003. Additional disclosure related to quinolinone compounds and uses thereof is set forth in U.S. Provisional Application No. 60/680,722, filed May 13, 2005; U.S. Provisional Application No. 60/681,893, filed May 17, 2005; U.S. Provisional Application No. 60/546,395, filed Feb. 20, 2004; U.S. Provisional Application No. 60/547,103, filed Feb. 23, 2004; U.S. Provisional Application No. 60/554,771, filed Mar. 19, 2004; U.S. Provisional Application No. 60/647,568, filed Jan. 27, 2005; U.S. Provisional Application No. 60/669,245, filed Apr. 6, 2005; U.S. Provisional Application No. 60/538,594, filed Jan. 23, 2004; U.S. Provisional Application No. 60/683,999; filed May 23, 3005; U.S. patent application Ser. No. 11/061,386, filed Feb. 18, 2005; U.S. patent application Ser. No. 11/041,191, filed Jan. 21, 2005; and PCT Application No. PCT/US2005/05316, filed Feb. 18, 2005. Heterocyclic compounds related to benzimidazolyl quinolinones have recently been disclosed in WO 02/18383, U.S. 2002/0103230, and U.S. Pat. No. 6,756,383. Each of the references in this paragraph is hereby incorporated by reference in its entirety and for all purposes as if fully set forth herein.
  • The SU-5402 compound is 3-[3-(2-Carboxyethyl)-4-methylpyrrol-2-methylidenyl]-2-indolinone and has the following formula.
  • Figure US20120149714A1-20120614-C00002
  • The PD-173074 compound has the compound structure and chemical name shown below.
  • Figure US20120149714A1-20120614-C00003
  • 1-tert-butyl-3-[6-(3,5-dimethoxyphenyl)-2-(4-diethylaminobutylamino)-pyrido[2,3-d]pyrimidin-7-yl]-urea.
    • Measurement of Gene Expression
  • As noted previously, the measurement of gene expression is performed on a sample, preferably a biological sample, obtained from the patient. For example, the patient may undergo a blood draw or tissue biopsy and the measurement may be made on the resulting sample. Depending upon the technique utilized, the test may be performed on an isolated fraction of the sample or in situ.
  • Detection of the presence of gene expression of the biomarker of interest and/or detection of the level of alteration in the gene expression compared to baseline may be made utilizing standard techniques.
  • Detection can be by any appropriate method, including for example, detecting the quantity of mRNA transcribed from the gene or the quantity of cDNA produced from the reverse transcription of the mRNA transcribed from the gene or the quantity of the polypeptide or protein encoded by the gene. These methods can be performed on a sample by sample basis or modified for high throughput analysis. Additionally, databases containing quantitative full or partial transcripts or protein sequences isolated from a cell sample can be searched and analyzed for the presence and amount of transcript or expressed gene product.
  • In assaying for an alteration in mRNA level, nucleic acid contained in the aforementioned samples is first extracted according to standard methods in the art. For instance, mRNA can be isolated using various lytic enzymes or chemical solutions according to the procedures set forth in Sambrook et al. (1989), supra or extracted by nucleic-acid-binding resins following the accompanying instructions provided by manufactures. The mRNA of the biomarker contained in the extracted nucleic acid sample is then detected by hybridization (e.g. Northern blot analysis) and/or amplification procedures according to methods widely known in the art or based on the methods exemplified herein.
  • Nucleic acid molecules having at least 10 nucleotides and exhibiting sequence complementarity or homology to the biomarkers described herein find utility as hybridization probes. It is known in the art that a “perfectly matched” probe is not needed for a specific hybridization. Minor changes in probe sequence achieved by substitution, deletion or insertion of a small number of bases do not affect the hybridization specificity. In general, as much as 20% base-pair mismatch (when optimally aligned) can be tolerated.
  • In certain embodiments, it will be advantageous to employ probes or primers in combination with an appropriate means, such as a label, for detecting hybridization and therefore complementary sequences. A wide variety of appropriate indicator means are known in the art, including fluorescent, radioactive, enzymatic or other ligands, such as avidin/biotin, which are capable of giving a detectable signal. In preferred embodiments, one will likely desire to employ a fluorescent label or an enzyme tag, such as urease, alkaline phosphatase or peroxidase, instead of radioactive or other environmental undesirable reagents. In the case of enzyme tags, colorimetric indicator substrates are known which can be employed to provide a means visible to the human eye or spectrophotometrically, to identify specific hybridization with complementary nucleic acid-containing samples.
  • Hybridization reactions can be performed under conditions of different “stringency”. Relevant conditions include temperature, ionic strength, time of incubation, the presence of additional solutes in the reaction mixture such as formamide, and the washing procedure. Higher stringency conditions are those conditions, such as higher temperature and lower sodium ion concentration, which require higher minimum complementarity between hybridizing elements for a stable hybridization complex to form. Conditions that increase the stringency of a hybridization reaction are widely known and published in the art. See, for example, (Sambrook, et al., (1989), supra).
  • Briefly, multiple RNAs are isolated from cell or tissue samples as described above. Optionally, the gene transcripts can be converted to cDNA. A sampling of the biomarker transcript(s) is/are subjected to sequence-specific analysis and quantified. These gene transcript sequence abundances are compared to the baseline.
  • Alternatively any one of gene copy number, transcription, or translation of a biomarker can be determined using an amplification method such as PCR. General procedures for PCR are taught in MacPherson et al., PCR: A PRACTICAL APPROACH, (IRL Press at Oxford University Press (1991)). However, PCR conditions used for each application reaction are empirically determined. A number of parameters influence the success of a reaction. Among them are annealing temperature and time, extension time, Mg2+ ATP concentration, pH, and the relative concentration of primers, templates, and deoxyribonucleotides. After amplification, the resulting DNA fragments can be detected by agarose gel electrophoresis followed by visualization with ethidium bromide staining and ultraviolet illumination.
  • In one aspect, the biomarkers are detected and quantitated by hybridization to a probe that specifically hybridizes to the appropriate probe for that biomarker. The probes also can be attached to a solid support for use in high throughput screening assays using methods known in the art. PCT WO 97/10365 and U.S. Pat. Nos. 5,405,783, 5,412,087 and 5,445,934, for example, disclose the construction of high density oligonucleotide chips which can contain one or more of the sequences disclosed herein. Using the methods disclosed in U.S. Pat. Nos. 5,405,783, 5,412,087 and 5,445,934 the probes of this invention are synthesized on a derivatized glass surface. Photoprotected nucleoside phosphoramidites are coupled to the glass surface, selectively deprotected by photolysis through a photolithographic mask, and reacted with a second protected nucleoside phosphoramidite. The coupling/deprotection process is repeated until the desired probe is complete.
  • In one aspect, the expression level of the biomarker is determined through exposure of a nucleic acid sample to the probe-modified chip. Extracted nucleic acid is labeled, for example, with a fluorescent tag, preferably during an amplification step. Hybridization of the labeled sample is performed at an appropriate stringency level. The degree of probe-nucleic acid hybridization is quantitatively measured using a detection device, such as a confocal microscope. See U.S. Pat. Nos. 5,578,832 and 5,631,734.
  • In an alternative embodiment, the method is performed by the detecting and comparing of two or more biomarkers that have been pre-determined to be predictive of a therapeutic response. In a yet further embodiment, a plurality of biomarkers, e.g., see Tables I through V, supra, are used in the method of this invention. In these embodiments, the biomarkers or probes that specifically hybridize and recognize the biomarker of interest are arranged on a high density oligonucleotide probe array that provides an effective means of monitoring expression of a multiplicity of genes.
  • In another preferred embodiment, the methods of this invention are used to monitor expression of the genes which specifically hybridize to the probes of this invention in so response to defined stimuli, such as a drug or biologic.
  • In one embodiment, the hybridized nucleic acids are detected by detecting one or more labels attached to the sample nucleic acids. The labels may be incorporated by any of a number of means well known to those of skill in the art. However, in one aspect, the label is simultaneously incorporated during the amplification step in the preparation of the sample nucleic acid. Thus, for example, polymerase chain reaction (PCR) with labeled primers or labeled nucleotides will provide a labeled amplification product. In a separate embodiment, transcription amplification, as described above, using a labeled nucleotide (e.g. fluorescein-labeled UTP and/or CTP) incorporates a label in to the transcribed nucleic acids.
  • Alternatively, a label may be added directly to the original nucleic acid sample (e.g., mRNA, polyA, mRNA, cDNA, etc.) or to the amplification product after the amplification is completed. Means of attaching labels to nucleic acids are well known to those of skill in the art and include, for example nick translation or end-labeling (e.g. with a labeled RNA) by kinasing of the nucleic acid and subsequent attachment (ligation) of a nucleic acid linker joining the sample nucleic acid to a label (e.g., a fluorophore).
  • Detectable labels suitable for use in the present invention include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Useful labels in the present invention include biotin for staining with labeled streptavidin conjugate, magnetic beads (e.g., Dynabeads™), fluorescent dyes (e.g., fluorescein, texas red, rhodamine, green fluorescent protein, and the like), radiolabels (e.g., 3H, 125I, 35S, 14C, or 32P) enzymes (e.g., horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (e.g., polystyrene, polypropylene, latex, etc.) beads. Patents teaching the use of such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149; and 4,366,241.
  • Means of detecting such labels are well known to those of skill in the art. Thus, for example, radiolabels may be detected using photographic film or scintillation counters, fluorescent markers may be detected using a photodetector to detect emitted light. Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label.
  • As described in more detail in WO 97/10365, the label may be added to the target (sample) nucleic acid(s) prior to, or after the hybridization. These are detectable labels that are directly attached to or incorporated into the target (sample) nucleic acid prior to hybridization. In contrast, “indirect labels” are joined to the hybrid duplex after hybridization. Often, the indirect label is attached to a binding moiety that has been attached to the target nucleic acid prior to the hybridization. Thus, for example, the target nucleic acid may be biotinylated before the hybridization. After hybridization, an avidin-conjugated fluorophore will bind the biotin bearing hybrid duplexes providing a label that is easily detected. Fore a detailed review of methods of labeling nucleic acids and detecting labeled hybridized nucleic acids see LABORATORY TECHNIQUES IN BIOCHEMISTRY AND MOLECULAR BIOLOGY, Vol. 24: Hybridization with Nucleic Acid Probes, P. Tijssen, ed. Elsevier, N.Y. (1993).
  • The nucleic acid sample also may be modified prior to hybridization to the high density probe array in order to reduce sample complexity thereby decreasing background signal and improving sensitivity of the measurement using the methods disclosed in WO 97/10365.
  • Results from the chip assay are typically analyzed using a computer software program. See, for example, EP 0717 113 A2 and WO 95/20681. The hybridization data is read into the program, which calculates the expression level of the targeted gene(s). The figures may be compared against existing data sets of gene expression levels for diseased and healthy individuals. A correlation between the obtained data and that of a set of a predetermined baseline identifies patients likely to be responsive to the therapy.
  • Also within the scope of this application is a data base useful for the identification of patients likely to respond to a predetermined therapy, e.g., anti-FGFR3 therapy, wherein the database contains a combination of base line gene expression data against which the patient sample can be compared using bioinformatic techniques known in the art.
  • The pre-determined baseline information is stored in a digital storage medium such that a data processing system for standardized representation of the genes that identify patients that are responsive to therapy. The data processing system is useful to analyze gene expression between two samples. A suitable sample is isolated from the patient and then the genotype or phenotype of the cell or sample is determined using methods known in the art. In one aspect, the nucleic acids of the biomarkers if present in the sample are sequenced and transcribed to code. The sequences (in code form) from the sample are compared with the sequence(s) present in the database using homology search techniques. Greater than 90%, or alternatively, greater than 95% or alternatively, greater than or equal to 97% sequence identity between the test sequence and at least one sequence identified by the biomarkers identified in Tables I through V is a positive indication that the polynucleotide from a biomarker has been isolated from the patient sample.
  • Expression level of the biomarker can also be determined by examining the protein product. Determining the protein level involves (a) providing a biological sample containing expression product of the biomarker; and (b) measuring the amount of any immunospecific binding that occurs between an antibody that selectively recognizes and binds to the expression product of the biomarker in the sample, in which the amount of immunospecific binding indicates the level of the biomarker expression. This information is then compared to a pre-determined base line and analyzed to identify those patients suitable for therapy.
  • A variety of techniques are available in the art for protein analysis. They include but are not limited to radioimmunoassays, ELISA (enzyme linked immunoradiometric assays), “sandwich” immunoassays, immunoradiometric assays, in situ immunoassays (using e.g., colloidal gold, enzyme or radioisotope labels), western blot analysis, immunoprecipitation assays, immunoflourescent assays, and PAGE-SDS.
  • Antibodies that specifically recognize and bind to the protein products of the expression products of the biomarkers are required for immunoassays. These may be purchased from commercial vendors or generated and screened using methods well known in the art. See Harlow and Lane (1988) supra. and Sambrook et al. (1989) supra.
    • Treatment
  • Inhibition of activated FGFR3 has been shown to induce apoptosis (Trudel, et al., Blood, 105(7):2941-2948 (2005)) A patient may be beneficially treated by administration of an inhibitor of FGFR3, particularly a tyrosine kinase small molecule inhibitor (SMI) of FGFR3. Thus, treatment according to the invention may constitute administration of one or more small molecule FGFR3 inhibitors, such as those disclosed herein.
  • Alternatively, the small molecule inhibitors may be used in combination with other treatments. For instance, inhibitors that are not small molecules, e.g. biologicals, polynucleotides, gene therapy, etc. may be used for the ongoing treatment, in some cases, whereas the small molecule FGFR3 inhibitor may be used primarily as an initial aid in identifying candidates.
  • In another alternative, one inhibitor may be used prior to a gene expression level measurement step and another may be used subsequently.
  • The methods of the invention are useful for treatment of cellular proliferative disease and particularly neoplastic disease.
  • One disease model in which the genetic profiling methods taught herein are especially useful is multiple myeloma. A subset of approximately 15-20% of multiple myeloma patients have a chromosomal translocation denoted the t(4; 14) translocation that is associated with the ectopic expression of the receptor tyrosine kinase fibroblast growth factor receptor 3 (FGFR3). The t(4; 14) abnormality is typically diagnosed via a cytogenetic test, such as a fluorescence in situ hybridization (FISH) analysis, performed on a bone marrow aspirate taken from the patient. The t(4; 14) multiple myeloma patient has a poor prognosis, but the methods taught herein offer new hope in that they may be employed to great advantage to identify such patients for treatment with an FGFR3 inhibitor, monitor response to treatment in such patients, as well as to aid in the development of new and/or optimized FGFR3 inhibitors.
  • Therapeutic agents utilized according to this invention, include, but are not limited to small molecules. They may be polynucleotides, peptides, antibodies, antigen presenting cells and include immune effector cells that specifically recognize and lyse cells expressing the gene of interest. One can determine if a subject or patient will be beneficially treated by the use of agents by screening one or more of the agents against tumor cells isolated from the subject or patient using methods known in the art.
  • Various delivery systems are known and can be used to administer a therapeutic agent in accordance with the methods of the invention, e.g., encapsulation in liposomes, microparticles, microcapsules, expression by recombinant cells, receptor-mediated endocytosis (See e.g., Wu and Wu (1987) J. Biol. Chem. 262:4429-4432), construction of a therapeutic nucleic acid as part of a retroviral or other vector, etc. Methods of delivery include but are not limited to intra-arterial, intra-muscular, intravenous, intranasal and oral routes. In a specific embodiment, it may be desirable to administer pharmaceutical compositions locally to the area in need of treatment; this may be achieved by, for example, and not by way of limitation, local infusion during surgery, by injection or by means of a catheter.
  • Administration in vivo can be effected in one dose, continuously or intermittently throughout the course of treatment. Methods of determining the most effective means and dosage of administration are well known to those of skill in the art and will vary with the composition used for therapy, the purpose of the therapy, the target cell being treated and the subject being treated. Single or multiple administrations can be carried out with the dose level and pattern being selected by the treating physician. Suitable dosage formulations and methods of administering the agents may be empirically adjusted.
  • Pharmaceutical compositions utilized according to the methods of the invention can be administered orally, intranasally, parenterally or by inhalation therapy, and may take the form of tablets, lozenges, granules, capsules, pills, ampoules, suppositories or aerosol form. They may also take the form of suspensions, solutions and emulsions of the active ingredient in aqueous or nonaqueous diluents, syrups, granulates or powders. In addition to the key active ingredients, the pharmaceutical compositions can also contain other pharmaceutically active compounds or a plurality of compositions of the invention.
  • More particularly, an agent administered according to the invention may be administered for therapy by any suitable route including oral, rectal, nasal, topical (including transdermal, aerosol, buccal and sublingual), vaginal, parental (including subcutaneous, intramuscular, intravenous and intradermal) and pulmonary. It will also be appreciated that the preferred route will vary with the condition and age of the recipient and the disease being treated.
  • Ideally, the agent should be administered to achieve peak concentrations of the active compound at sites of disease. This may be achieved, for example, by the intravenous injection of the agent, optionally in saline or orally administered, for example, as a tablet, capsule or syrup containing the active ingredient. Desirable blood levels of the agent may be maintained by a continuous infusion to provide a therapeutic amount of the active ingredient within disease tissue. The use of operative combinations is contemplated to provide therapeutic combinations requiring a lower total dosage of each component antiviral agent than may be required when each individual therapeutic compound or drug is used alone, thereby reducing adverse effects.
  • While it is possible for the agent to be administered alone, it is preferable to present it as a pharmaceutical formulation comprising at least one active ingredient, as defined above, together with one or more pharmaceutically acceptable carriers therefor and optionally other therapeutic agents. Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient.
  • Formulations include those suitable for oral, rectal, nasal, topical (including transdermal, buccal and sublingual), vaginal, parenteral (including subcutaneous, intramuscular, intravenous and intradermal) and pulmonary administration. The formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. Such methods include the step of bringing into association the active ingredient with the carrier which constitutes one or more accessory ingredients. In general, the formulations are prepared by uniformly and intimately bringing into association the active ingredient with liquid carriers or finely divided solid carriers or both and then, if necessary, shaping the product.
  • Formulations suitable for oral administration may be presented as discrete units such as capsules, cachets or tablets, each containing a predetermined amount of the active ingredient; as a powder or granules; as a solution or suspension in an aqueous or non-aqueous liquid; or as an oil-in-water liquid emulsion or a water-in-oil liquid emulsion. The active ingredient may also be presented a bolus, electuary or paste.
  • A tablet may be made by compression or molding, optionally with one or more accessory ingredients. Compressed tablets may be prepared by compressing in a suitable machine the active ingredient in a free-flowing form such as a powder or granules, optionally mixed with a binder (e.g., povidone, gelatin, hydroxypropylmethyl cellulose), lubricant, inert diluent, preservative, disintegrant (e.g., sodium starch glycolate, cross-linked povidone, cross-linked sodium carboxymethyl cellulose) surface-active or dispersing agent. Molded tablets may be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent. The tablets may optionally be coated or scored and may be formulated so as to provide slow or controlled release of the active ingredient therein using, for example, hydroxypropylmethyl cellulose in varying proportions to provide the desired release profile. Tablets may optionally be provided with an enteric coating, to provide release in parts of the gut other than the stomach.
  • Formulations suitable for topical administration in the mouth include lozenges comprising the active ingredient in a flavored basis, usually sucrose and acacia or tragacanth; pastilles comprising the active ingredient in an inert basis such as gelatin and glycerin or sucrose and acacia; and mouthwashes comprising the active ingredient in a suitable liquid carrier.
  • Pharmaceutical compositions for topical administration according to the present invention may be formulated as an ointment, cream, suspension, lotion, powder, solution, past, gel, spray, aerosol or oil. Alternatively, a formulation may comprise a patch or a dressing such as a bandage or adhesive plaster impregnated with active ingredients and optionally one or more excipients or diluents.
  • If desired, the aqueous phase of the cream base may include, for example, at least about 30% w/w of a polyhydric alcohol, i.e., an alcohol having two or more hydroxyl groups such as propylene glycol, butane-1,3-diol, mannitol, sorbitol, glycerol and polyethylene glycol and mixtures thereof. The topical formulations may desirably include a compound which enhances absorption or penetration of the agent through the skin or other affected areas. Examples of such dermal penetration enhancers include dimethylsulfoxide and related analogues.
  • The oily phase of the emulsions of a composition used according to this invention may be constituted from known ingredients in a known manner. While this phase may comprise merely an emulsifier (otherwise known as an emulgent), it desirably comprises a mixture of at least one emulsifier with a fat or an oil or with both a fat and an oil. Preferably, a hydrophilic emulsifier is included together with a lipophilic emulsifier which acts as a stabilizer. It is also preferred to include both an oil and a fat. Together, the emulsifier(s) with or without stabilizer(s) make up the so-called emulsifying wax, and the wax together with the oil and/or fat make up the so-called emulsifying ointment base which forms the oily dispersed phase of the cream formulations.
  • Emulgents and emulsion stabilizers suitable for use in the formulation of the present invention include Tween 60, Span 80, cetostearyl alcohol, myristyl alcohol, glyceryl monostearate and sodium lauryl sulphate.
  • The choice of suitable oils or fats for the formulation is based on achieving the desired cosmetic properties, since the solubility of the active compound in most oils likely to be used in pharmaceutical emulsion formulations is very low. Thus the cream should preferably be a non-greasy, non-staining and washable product with suitable consistency to avoid leakage from tubes or other containers. Straight or branched chain, mono- or dibasic alkyl esters such as di-isoadipate, isocetyl stearate, propylene glycol diester of coconut fatty acids, isopropyl myristate, decyl oleate, isopropyl palmitate, butyl stearate, 2-ethylhexyl palmitate or a blend of branched chain esters known as Crodamol CAP may be used, the last three being preferred esters. These may be used alone or in combination depending on the properties required.
  • Alternatively, high melting point lipids such as white soft paraffin and/or liquid paraffin or other mineral oils can be used.
  • Formulations suitable for topical administration to the eye also include eye drops wherein the active ingredient is dissolved or suspended in a suitable carrier, especially an aqueous solvent for the agent.
  • Formulations for rectal administration may be presented as a suppository with a suitable base comprising, for example, cocoa butter or a salicylate.
  • Formulations suitable for vaginal administration may be presented as pessaries, tampons, creams, gels, pastes, foams or spray formulations containing in addition to the agent, such carriers as are known in the art to be appropriate.
  • Formulations suitable for nasal administration, wherein the carrier is a solid, include a coarse powder having a particle size, for example, in the range of about 20 to about 500 microns which is administered in the manner in which snuff is taken, i.e., by rapid inhalation through the nasal passage from a container of the powder held close up to the nose. Suitable formulations wherein the carrier is a liquid for administration as, for example, nasal spray, nasal drops or by aerosol administration by nebulizer, include aqueous or oily solutions of the agent.
  • Formulations suitable for parenteral administration include aqueous and non-aqueous isotonic sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents, thickening agents and liposomes or other microparticulate systems which are designed to target the compound to blood components or one or more organs. The formulations may be presented in unit-dose or multi-dose sealed containers, for example, ampoules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example water for injections, immediately prior to use. Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets of the kind previously described.
  • Preferred unit dosage formulations are those containing a daily dose or unit, daily subdose, as herein above-recited, or an appropriate fraction thereof, of an agent.
    • Experimental Example
  • Transcriptional activity was assessed by measuring levels of messenger RNA (mRNA) in cells derived from human multiple myeloma tumors using Affymetrix HG-U133-Plus-2 GeneChips.
  • Expression of mRNA in cells treated with the small molecule inhibitors SU-5402, PD-173074 (both Pfizer Inc.) and CHIR-258 (Chiron Corp.), with FGF ligand, or with FGFR3 silencing RNA (siRNA) was quantitatively compared to expression in untreated cells (or cells treated with a scrambled siRNA control in the latter case). Specific differences and similarities to the other FGFR3 inhibitors were compared with CHIR-258.
  • The following multiple myeloma cell lines were used:
      • KMS11: Ras WT, FGFR3Y373C mutant; sensitive to CHIR-258 treatment
      • KMS18: Ras WT, FGFR3G384D mutant; sensitive to CHIR-258 treatment
      • H929: N13 Ras mutant, FGFR3 wild-type (WT); resistant to CHIR-258 treatment
      • U266: Ras WT, FGFR3 negative; resistant to CHIR-258 treatment
      • UTMC2: Ras WT, FGFR3WT; resistant to CHIR-258 treatment
        Bioinformatics analysis was performed on the raw data to provide the results.
  • Changes in gene expression level in response to the various FGFR3 inhibitors tested and deemed to be of statistical significance were utilized to generate Table I disclosed herein, and its various subsets. Within the parameters of this experiment, the biomarkers of Table I generally correlate with alterations in expression level of one-and-a-half-fold or greater, whereas the biomarkers of Table II generally correlate with alterations in expression level of two-fold or greater, and the biomarkers of Table III generally correlate with alterations in expression level of four-fold or greater. Table IV was generated with data showing alterations in gene expression in response to FGFR3 inhibition in the relevant cell lines of the experiment by the preferred compound, CHIR-258. Table V was generated with data showing alterations in gene expression in response to FGFR3 inhibition in the relevant cell lines of the experiment by the preferred compound, CHIR-258, but not to any significant extent by the other small molecule inhibitors tested.

Claims (66)

1. A method of identifying a patient for treatment, the method comprising:
administering an amount of an inhibitor of FGFR3 to the patient, and
testing a sample obtained from the patient after the administration of the inhibitor to measure gene expression of at least one biomarker selected from Table I,
wherein detection of an alteration in level of expression compared to baseline of the at least one biomarker is indicative of the candidacy of the patient for treatment.
2. A method of identifying a patient for treatment, the method comprising:
testing a sample obtained from a patient to measure gene expression of at least one biomarker selected from Table I,
wherein detection of the presence of gene expression of the at least one biomarker is indicative of the candidacy of the patient for treatment.
3. A method of monitoring response of a patient in need thereof to treatment for a cell proliferative disorder, the method comprising:
administering an amount of an inhibitor of FGFR3 to the patient,
testing a sample obtained from the patient after the administration of the inhibitor to measure gene expression of at least one biomarker selected from Table I,
wherein detection of an alteration in level of expression of the at least one biomarker is compared to baseline is indicative of a favorable response of the patient to the treatment.
4. A method of monitoring response of a patient to treatment by an inhibitor of FGFR3 for a cell proliferative disorder, the method comprising:
testing a sample obtained from the patient to measure gene expression of at least one biomarker selected from Table I,
wherein detection of an alteration in level of expression of the at least one biomarker compared to baseline is indicative of a favorable response of the patient to the treatment.
5. A method of utilizing a biomarker in treatment of a cell proliferative disorder in a patient, the method comprising
administering an amount of an inhibitor of FGFR3 to the patient,
testing a sample obtained from the patient to measure gene expression of at least one biomarker selected from Table I, and
subsequently administering the same or a different inhibitor of FGFR3 to the patient provided favorable alteration of the level of expression of the at least one biomarker is detected upon administration of the initial inhibitor.
6. A method of treating a multiple myeloma patient, the method comprising administering a therapeutically effective amount of an agent that alters the level of expression compared to baseline of a biomarker identified in Table I, thereby inhibiting abnormalities associated with multiple myeloma.
7. A method of adjusting a dosage amount of an inhibitor of FGFR3 for treatment of a cell proliferative disorder in a patient, the method comprising:
administering an initial amount of the inhibitor of FGFR3 to the patient,
monitoring gene expression of at least one biomarker selected from Table I after the administration of the initial amount of the inhibitor, and
adjusting the amount for subsequent administration of the inhibitor to the patient based upon the level of alteration of the expression of the biomarker or biomarkers that has occurred upon administration of the initial amount.
8. A method of utilizing a biomarker to identify an FGFR3 inhibitory compound for potential treatment of multiple myeloma or to guide a decision to progress an FGFR3 inhibitory compound to further development for treatment of multiple myeloma, the method comprising:
contacting the compound with a KMS18 or KMS11 cell culture, and
testing a portion of the cell culture to measure gene expression of at least one biomarker selected from Table I,
wherein detection of an alteration in expression of the at least one biomarker is indicative of an identification of the compound for treatment or a favorable decision to progress the compound for further development.
9. A method of selecting an appropriate inhibitor of FGFR3 to administer to a patient in need of treatment with said inhibitor, the method comprising:
administering an initial inhibitor of FGFR3 to the patient,
testing a sample obtained from the patient to measure gene expression of at least one biomarker selected from Table I, and
subsequently administering the initial inhibitor of FGFR3 to the patient provided favorable alteration of the level of expression of the at least one biomarker is detected upon administration of the initial inhibitor.
10. A method of utilizing a biomarker to identify an FGFR3 inhibitory compound for potential treatment of a cell proliferative disorder, the method comprising:
contacting the compound with a cell line or tissue associated with the disorder, and
testing a portion of the cell culture or tissue after the contacting to measure gene expression of at least one biomarker that has been altered compared to baseline,
wherein detection of an alteration in expression of the at least one biomarker is indicative of an identification of the compound for treatment.
11. The method of claim 1, wherein detection of an alteration in level of expression compared to baseline of at least one biomarker selected from a subset of Table I represented by Table II is indicative of the candidacy of the patient for treatment.
12. The method of claim 1, wherein detection of an alteration in level of expression compared to baseline of at least one biomarker selected from a subset of Table I represented by Table III is indicative of the candidacy of the patient for treatment.
13. The method of claim 1, wherein detection of an alteration in level of expression compared to baseline of at least one biomarker selected from a subset of Table I represented by Table IV is indicative of the candidacy of the patient for treatment.
14. The method of claim 1, wherein detection of an alteration in level of expression compared to baseline of at least one biomarker selected from a subset of Table I represented by Table V is indicative of the candidacy of the patient for treatment.
15. The method of claim 1, wherein detection of an alteration in level of expression compared to baseline of at least two biomarkers selected from a subset of Table I represented by Table II is indicative of the candidacy of the patient for treatment.
16. The method of claim 1, wherein the measurement of gene expression is made by detecting the quantity of RNA transcribed by the biomarker.
17. The method of claim 1, wherein the measurement of gene expression is made by detecting the quantity of DNA produced from reverse transcription of an RNA transcribed by the biomarker.
18. The method of claim 1, wherein the measurement of gene expression is made by detecting a polypeptide or protein encoded by the biomarker.
19. The method of claim 1, wherein the at least one biomarker is operably linked to a gene chip.
20. The method of claim 1, wherein the at least one biomarker is represented in computer readable format.
21. The method of claim 1, wherein the testing comprises contacting the sample with a gene chip comprising the biomarkers of any one of Tables I through V.
22. The method of claim 1, wherein the detecting step comprises comparing the gene expression level of the biomarker with a gene database.
23. The method of claim 1, wherein the treatment comprises administration of a therapeutically effective amount of the same or a different inhibitor of FGFR3 to the patient.
24. The method of claim 1, wherein the treatment is for a cell proliferative disorder.
25. The method of claim 1, wherein the treatment is for a neoplastic disease.
26. The method of claim 1, wherein the treatment is for multiple myeloma.
27. The method of claim 1, wherein the treatment is for t(4; 14) multiple myeloma.
28. The method of claim 1, wherein the inhibitor is selected from the group consisting of CHIR-258, SU-5402, and PD-173074.
29. The method of claim 1, wherein the inhibitor is CHIR-258.
30. The method of claim 1, wherein the biomarker is selected from the group consisting of CCL3, LOC150271, CD48, DUSP4, and ITGB7.
31. The method of claim 1, wherein the biomarker is selected from the group consisting of LOC150271, CD48, DUSP4, and ITGB7.
32. The method of claim 1, wherein the biomarker is CCL3.
33. (canceled)
34. The method of claim 1, further comprising establishing a baseline level for the patient prior to administering the FGFR3 inhibitor.
35. The method of claim 3, wherein detection of an alteration in level of expression compared to baseline of at least one biomarker selected from a subset of Table I represented by Table II is indicative of a favorable response of the patient to the treatment.
36. The method of claim 3, wherein detection of an alteration in level of expression compared to baseline of at least one biomarker selected from a subset of Table I represented by Table III is indicative of a favorable response of the patient to the treatment.
37. The method of claim 3, wherein detection of an alteration in level of expression compared to baseline of at least one biomarker selected from a subset of Table I represented by Table IV is indicative of a favorable response of the patient to the treatment.
38. The method of claim 3, wherein detection of an alteration in level of expression compared to baseline of at least one biomarker selected from a subset of Table I represented by Table V is indicative of a favorable response of the patient to treatment.
39. The method of claim 3, wherein detection of an alteration in level of expression compared to baseline of at least two biomarkers selected from a subset of Table I represented by Table II is indicative of a favorable response of the patient to the treatment.
40. The method of claim 3, wherein the administering step is repeated before the step of testing a sample obtained from the patient.
41. The method of claim 3, wherein the inhibitor of FGFR3 is administered in a therapeutically effective amount.
42. The method of claim 5, wherein favorable alteration of the level of expression comprises alteration compared to baseline of at least one biomarker selected from a subset of Table I represented by Table II.
43. The method of claim 5, wherein favorable alteration of the level of expression comprises alteration compared to baseline of at least one biomarker selected from a subset of Table I represented by Table III.
44. The method of claim 5, wherein favorable alteration of the level of expression comprises alteration compared to baseline of at least one biomarker selected from a subset of Table I represented by Table IV.
45. The method of claim 5, wherein favorable alteration of the level of expression comprises alteration compared to baseline of at least one biomarker selected from a subset of Table I represented by Table V.
46. The method of claim 5, wherein favorable alteration of the level of expression comprises alteration compared to baseline of at least two biomarkers selected from a subset of Table I represented by Table II.
47. The method of claim 5, wherein the initial inhibitor and the subsequently administered inhibitor are each selected from the group consisting of CHIR-258, SU-5402, and PD-173074.
48. The method of claim 5, wherein the initial inhibitor is CHIR-258.
49. The method of claim 5, wherein the subsequently administered inhibitor is CHIR-258.
50. (canceled)
51. The method of claim 6, wherein the alteration compared to baseline of at least one biomarker is selected from a subset of Table I represented by Table II.
52. The method of claim 6, wherein the alteration compared to baseline is of at least one biomarker selected from a subset of Table I represented by Table III.
53. The method of claim 6, wherein the alteration compared to baseline is of at least one biomarker selected from a subset of Table I represented by Table IV.
54. The method of claim 6, wherein the alteration compared to baseline is of at least one biomarker selected from a subset of Table I represented by Table V.
55. The method of claim 6, wherein the alteration compared to baseline of at least two biomarkers selected from a subset of Table I represented by Table II.
56. The method of claim 6, wherein the agent is CHIR-258.
57. The method of claim 6, wherein the patient is a t(4:14) multiple myeloma patient.
58. The method of claim 7, wherein the gene expression is monitored for at least one biomarker selected from a subset of Table I represented by Table II.
59. The method of claim 7, wherein the gene expression is monitored for at least one biomarker selected from a subset of Table I represented by Table III.
60. The method of claim 7, wherein the gene expression is monitored for at least one biomarker selected from a subset of Table I represented by Table IV.
61. The method of claim 7, wherein the gene expression is monitored for at least one biomarker selected from a subset of Table I represented by Table V.
62. The method of claim 7, wherein the monitoring comprises contacting the sample with a gene chip comprising the biomarkers of any one of Tables I through V and comparing the gene expression level of the biomarker with a gene database.
63. The method of claim 10, wherein the biomarker is selected from Table I.
64. A method of identifying a patient for treatment, the method comprising:
administering an amount of an inhibitor of FGFR3 to the patient, and
testing a sample obtained from the patient after the administration of the inhibitor to measure gene expression of at least one biomarker selected from the group consisting of CCL3, DUSP6, ANXA9, CR2, AL531683, ZNF589, AW274468, FRMD3, LTB, and WDR42A,
wherein detection of an alteration in level of expression compared to baseline of the at least one biomarker is indicative of the candidacy of the patient for treatment.
65. A method of monitoring response of a patient to treatment by an inhibitor of FGFR3 for a cell proliferative disorder, the method comprising:
testing a sample obtained from the patient to measure gene expression of at least one biomarker selected from the group consisting of CCL3, DUSP6, ANXA9, CR2, AL531683, ZNF589, AW274468, FRMD3, LTB, and WDR42A,
wherein detection of an alteration in level of expression of the at least one biomarker compared to baseline is indicative of a favorable response of the patient to the treatment.
66. The method of claim 1, wherein the biomarker is not any or all of CCL3, DUSP6, ANXA9, CR2, AL531683, ZNF589, AW274468, FRMD3, LTB, and WDR42A.
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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US12331320B2 (en) 2018-10-10 2025-06-17 The Research Foundation For The State University Of New York Genome edited cancer cell vaccines

Families Citing this family (45)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2009131365A2 (en) * 2008-04-21 2009-10-29 한국생명공학연구원 Cst1, dcc1, ifitm1 or melk as markers for diagnosing stomach cancer
TWI526687B (en) * 2008-04-29 2016-03-21 諾華公司 Biomarkers
WO2009144311A1 (en) * 2008-05-29 2009-12-03 Vib Vzw Minichromosome maintenance complex interacting protein involved in cancer
US20120041274A1 (en) * 2010-01-07 2012-02-16 Myriad Genetics, Incorporated Cancer biomarkers
WO2011151321A1 (en) * 2010-05-31 2011-12-08 Institut Curie Asf1b as a prognosis marker and therapeutic target in human cancer
MX338883B (en) 2010-07-27 2016-05-04 Genomic Health Inc Method for using gene expression to determine prognosis of prostate cancer.
CA2807552A1 (en) 2010-08-06 2012-02-09 Moderna Therapeutics, Inc. Engineered nucleic acids and methods of use thereof
SMT202200321T1 (en) 2010-10-01 2022-09-14 Modernatx Inc Ribonucleic acids containing n1-methyl-pseudouracils and uses thereof
WO2012063875A1 (en) * 2010-11-11 2012-05-18 シスメックス株式会社 Markers for detecting human follicular helper t cells and method for detecting human follicular helper t cells
WO2012135805A2 (en) 2011-03-31 2012-10-04 modeRNA Therapeutics Delivery and formulation of engineered nucleic acids
US9464124B2 (en) 2011-09-12 2016-10-11 Moderna Therapeutics, Inc. Engineered nucleic acids and methods of use thereof
ES2911677T3 (en) 2011-10-03 2022-05-20 Modernatx Inc Nucleosides, nucleotides and modified nucleic acids, and their uses
US9206128B2 (en) 2011-11-18 2015-12-08 Constellation Pharmaceuticals, Inc. Modulators of methyl modifying enzymes, compositions and uses thereof
US20130156849A1 (en) 2011-12-16 2013-06-20 modeRNA Therapeutics Modified nucleoside, nucleotide, and nucleic acid compositions
NZ628762A (en) 2012-02-10 2016-07-29 Constellation Pharmaceuticals Inc Modulators of methyl modifying enzymes, compositions and uses thereof
US9878056B2 (en) 2012-04-02 2018-01-30 Modernatx, Inc. Modified polynucleotides for the production of cosmetic proteins and peptides
EP2834260A4 (en) 2012-04-02 2016-08-10 Moderna Therapeutics Inc MODIFIED POLYNUCLEOTIDES FOR THE PRODUCTION OF MEMBRANE PROTEINS
US9283287B2 (en) 2012-04-02 2016-03-15 Moderna Therapeutics, Inc. Modified polynucleotides for the production of nuclear proteins
US9572897B2 (en) 2012-04-02 2017-02-21 Modernatx, Inc. Modified polynucleotides for the production of cytoplasmic and cytoskeletal proteins
EP2902489B9 (en) * 2012-09-27 2018-02-07 Chugai Seiyaku Kabushiki Kaisha Fgfr3 fusion gene and pharmaceutical drug targeting same
HRP20220607T1 (en) 2012-11-26 2022-06-24 Modernatx, Inc. Terminally modified rna
WO2014151142A1 (en) 2013-03-15 2014-09-25 Constellation Pharmaceuticals, Inc. Modulators of methyl modifying enzymes, compositions and uses thereof
US8980864B2 (en) 2013-03-15 2015-03-17 Moderna Therapeutics, Inc. Compositions and methods of altering cholesterol levels
US9969716B2 (en) 2013-08-15 2018-05-15 Constellation Pharmaceuticals, Inc. Indole derivatives as modulators of methyl modifying enzymes, compositions and uses thereof
EA201690675A1 (en) 2013-10-03 2016-08-31 Модерна Терапьютикс, Инк. POLYNUCLEOTES ENCODING THE RECEPTOR OF LOW DENSITY LIPOPROTEINS
CN107002141B (en) * 2014-09-26 2021-11-02 詹森药业有限公司 Using FGFR mutant genomes to identify cancer patients who will respond to treatment with FGFR inhibitors
US11391744B2 (en) 2015-06-08 2022-07-19 Arquer Diagnostic Limited Methods and kits
CN107771285A (en) 2015-06-08 2018-03-06 阿奎尔诊断有限公司 Method
US10577350B2 (en) 2015-08-28 2020-03-03 Constellation Pharmaceuticals, Inc. Crystalline forms of (R)-N-((4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1-(1-(1-(2,2,2-trifluoroethyl)piperidin-4-yl)ethyl)-1H-indole-3-carboxamide
AU2017326253B2 (en) 2016-09-13 2021-10-21 Allergan, Inc. Stabilized non-protein clostridial toxin compositions
EP3529242A1 (en) 2016-10-19 2019-08-28 Constellation Pharmaceuticals, Inc. Synthesis of inhibitors of ezh2
KR20190142775A (en) 2017-04-19 2019-12-27 보드 오브 리전츠, 더 유니버시티 오브 텍사스 시스템 Immune Cells Expressing Engineered Antigen Receptors
CN107254474B (en) * 2017-06-16 2019-11-01 江苏省农业科学院 Sea island cotton Genes Encoding Transmembrane Proteins, primer and its application
CN107760765A (en) * 2017-11-29 2018-03-06 河南农业大学 A kind of method for detecting pig ADD2 gene expression amounts and application
CN108330094B (en) * 2018-01-10 2020-04-21 上海晶诺生物科技有限公司 Free recombinant mycobacterium smegmatis producing nicotinic acid and construction method thereof
US12473336B2 (en) 2018-02-21 2025-11-18 Board Of Regents, The University Of Texas System Methods for activation and expansion of natural killer cells and uses thereof
CA3121247A1 (en) 2018-12-03 2020-06-11 Board Of Regents, The University Of Texas System Oligo-benzamide analogs and their use in cancer treatment
CN110218789B (en) * 2019-04-22 2022-10-04 曾文炳 Gene probe composition and kit for predicting overall survival rate of multiple myeloma patients
CA3141871A1 (en) * 2019-05-31 2020-12-03 Qed Therapeutics, Inc. Methods of treating urinary system cancers
US10835531B1 (en) * 2019-06-18 2020-11-17 Oncology Venture ApS Methods for predicting drug responsiveness in cancer patients
CN111187841A (en) * 2020-03-11 2020-05-22 华东医院 Methylated molecular marker for diagnosing lung adenocarcinoma and application thereof
CN116323666A (en) 2020-08-21 2023-06-23 建新公司 FGFR3 antibodies and methods of use
CN115873955B (en) * 2022-12-22 2024-08-23 复旦大学附属中山医院 Kit for evaluating sensitivity of cisplatin to lung adenocarcinoma
CN116179703B (en) * 2023-02-16 2024-11-15 厦门艾德生物医药科技股份有限公司 Molecular marker for melanoma prognosis and application thereof
CN118441051B (en) * 2024-05-28 2025-05-02 南通大学 MeQTL-SNPs biomarker related to lung adenocarcinoma and application thereof

Family Cites Families (23)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
NL154598B (en) 1970-11-10 1977-09-15 Organon Nv PROCEDURE FOR DETERMINING AND DETERMINING LOW MOLECULAR COMPOUNDS AND PROTEINS THAT CAN SPECIFICALLY BIND THESE COMPOUNDS AND TEST PACKAGING.
US3817837A (en) 1971-05-14 1974-06-18 Syva Corp Enzyme amplification assay
US3939350A (en) 1974-04-29 1976-02-17 Board Of Trustees Of The Leland Stanford Junior University Fluorescent immunoassay employing total reflection for activation
US3996345A (en) 1974-08-12 1976-12-07 Syva Company Fluorescence quenching with immunological pairs in immunoassays
US4119105A (en) 1977-01-31 1978-10-10 Olin Corporation Air flow limiting filter
US4275149A (en) 1978-11-24 1981-06-23 Syva Company Macromolecular environment control in specific receptor assays
US4277437A (en) 1978-04-05 1981-07-07 Syva Company Kit for carrying out chemically induced fluorescence immunoassay
US4366241A (en) 1980-08-07 1982-12-28 Syva Company Concentrating zone method in heterogeneous immunoassays
US6040138A (en) 1995-09-15 2000-03-21 Affymetrix, Inc. Expression monitoring by hybridization to high density oligonucleotide arrays
US5143854A (en) 1989-06-07 1992-09-01 Affymax Technologies N.V. Large scale photolithographic solid phase synthesis of polypeptides and receptor binding screening thereof
US5412087A (en) 1992-04-24 1995-05-02 Affymax Technologies N.V. Spatially-addressable immobilization of oligonucleotides and other biological polymers on surfaces
US6114114A (en) 1992-07-17 2000-09-05 Incyte Pharmaceuticals, Inc. Comparative gene transcript analysis
US5578832A (en) 1994-09-02 1996-11-26 Affymetrix, Inc. Method and apparatus for imaging a sample on a device
US5631734A (en) 1994-02-10 1997-05-20 Affymetrix, Inc. Method and apparatus for detection of fluorescently labeled materials
US5795716A (en) 1994-10-21 1998-08-18 Chee; Mark S. Computer-aided visualization and analysis system for sequence evaluation
US6138605A (en) 1998-08-05 2000-10-31 Seascape Systems Limited Access and evacuation apparatus with articulated arm
PT1313734E (en) 2000-09-01 2010-02-09 Novartis Vaccines & Diagnostic Aza heterocyclic derivatives and their therapeutic use
US20030028018A1 (en) 2000-09-11 2003-02-06 Chiron Coporation Quinolinone derivatives
AU9327501A (en) 2000-09-11 2002-03-26 Chiron Corp Quinolinone derivatives
JP2005512557A (en) * 2001-11-07 2005-05-12 ザ ボード オブ トラスティーズ オブ ザ ユニヴァーシティー オブ アーカンソー Diagnosis, prognosis, and identification of therapeutic targets for multiple myeloma based on gene expression profiling
BR0313743A (en) 2002-08-23 2005-07-05 Chiron Corp Benzimidazole quinolinones and uses of these
BR0316229A (en) 2002-11-13 2005-10-04 Chiron Corp Cancer Treatment Methods and Related Methods
EP1692085A4 (en) 2003-11-07 2010-10-13 Novartis Vaccines & Diagnostic INHIBITION OF FGFR3 RECEPTOR AND TREATMENT OF MULTIPLE MYELOMA

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US12331320B2 (en) 2018-10-10 2025-06-17 The Research Foundation For The State University Of New York Genome edited cancer cell vaccines

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