Abstract:
Two hundred ten markers are provided which are epigenetically silenced in one or more cancer types. The markers can be used diagnostically, prognostically, therapeutically, and for selecting treatments that are well tailored for an individual patient. Restoration of expression of silenced genes can be useful therapeutically, for example, if the silenced gene is a tumor-suppressor gene. Restoration can be accomplished by supplying non-methylated copies of the silenced genes or polynucleotides encoding their encoded products. Alternatively, restoration can be accomplished using chemical demethylating agents or methylation inhibitors. Kits for testing for epigenetic silencing can be used in the context of diagnostics, prognostics, or for selecting “personalized medicine” treatments.

Description:
[0001]    This application incorporates by reference the contents of each of two duplicate CD-ROMs. Each CD-ROM contains an identical 1,720 kB file labeled “882832 — 1.txt” and containing the sequence listing for this application. Each CD-ROM also contains an identical 230 kB file labeled “882734 — 1.txt” containing TABLE 9; an identical 33 kB file labeled “882733 — 1.txt” containing TABLE 10; an identical 481 kB file labeled “882729 — 1” containing TABLE 11; an identical 450 kB file labeled “882730 — 1.txt” containing TABLE 12; an identical 2,458 kB file labeled “882732.txt” containing TABLE 13; and an identical 547 kB file labeled “882731 — 1.txt” containing TABLE 14. The CD-ROMs were created on Apr. 11, 2006. 
         [0002]    This application claims the benefit of U.S. provisional application Ser. No. 60/671,501, filed Apr. 15, 2005. 
     
    
     TECHNICAL FIELD OF THE INVENTION 
       [0003]    This invention is related to the area of cancer diagnostics and therapeutics. In particular, it relates to aberrant methylation patterns of particular genes in cancers. 
       BACKGROUND OF THE INVENTION 
       [0004]    DNA Methylation and its Role in Carcinogenesis 
         [0005]    The information to make the cells of all living organisms is contained in their DNA. DNA is made up of a unique sequence of four bases: adenine (A), guanine (G), thymine (T) and cytosine (C). These bases are paired A to T and G to C on the two strands that form the DNA double helix. Strands of these pairs store information to make specific molecules grouped into regions called genes. Within each cell, there are processes that control what gene is turned on, or expressed, thus defining the unique function of the cell. One of these control mechanisms is provided by adding a methyl group onto cytosine (C). The methyl group tagged C can be written as mC. 
         [0006]    DNA methylation plays an important role in determining whether some genes are expressed or not. By turning genes off that are not needed, DNA methylation is an essential control mechanism for the normal development and functioning of organisms. Alternatively, abnormal DNA methylation is one of the mechanisms underlying the changes observed with aging and development of many cancers. 
         [0007]    Cancers have historically been linked to genetic changes caused by chromosomal mutations within the DNA. Mutations, hereditary or acquired, can lead to the loss of expression of genes critical for maintaining a healthy state. Evidence now supports that a relatively large number of cancers originate, not from mutations, but from inappropriate DNA methylation. In many cases, hyper-methylation of DNA incorrectly switches off critical genes, such as tumor suppressor genes or DNA repair genes, allowing cancers to develop and progress. This non-mutational process for controlling gene expression is described as epigenetics. 
         [0008]    DNA methylation is a chemical modification of DNA performed by enzymes called methyltransferases, in which a methyl group (m) is added to certain cytosines (C) of DNA. This non-mutational (epigenetic) process (mC) is a critical factor in gene expression regulation. See, J. G. Herman, Seminars in Cancer Biology, 9: 359-67, 1999. 
         [0009]    Although the phenomenon of gene methylation has attracted the attention of cancer researchers for some time, its true role in the progression of human cancers is just now being recognized. In normal cells, methylation occurs predominantly in regions of DNA that have few CG base repeats, while CpG islands, regions of DNA that have long repeats of CG bases, remain non-methylated. Gene promoter regions that control protein expression are often CpG island-rich. Aberrant methylation of these normally non-methylated CpG islands in the promoter region causes transcriptional inactivation or silencing of certain tumor suppressor expression in human cancers. 
         [0010]    Genes that are hypermethylated in tumor cells are strongly specific to the tissue of origin of the tumor. Molecular signatures of cancers of all types can be used to improve cancer detection, the assessment of cancer risk and response to therapy. Promoter hypermethylation events provide some of the most promising markers for such purposes. 
         [0011]    Promoter Gene Hypermethylation: Promising Tumor Markers 
         [0012]    Information regarding the hypermethylation of specific promoter genes can be beneficial to diagnosis, prognosis, and treatment of various cancers. Methylation of specific gene promoter regions can occur early and often in carcinogenesis malting these markers ideal targets for cancer diagnostics. 
         [0013]    Methylation patterns are tumor specific. Positive signals are always found in the same location of a gene. Real time PCR-based methods are highly sensitive, quantitative, and suitable for clinical use. DNA is stable and is found intact in readily available fluids (e.g., serum, sputum, stool and urine) and paraffin embedded tissues. Panels of pertinent gene markers may cover most human cancers. 
         [0014]    Diagnosis 
         [0015]    Key to improving the clinical outcome in patients with cancer is diagnosis at its earliest stage, while it is still localized and readily treatable. The characteristics noted above provide the means for a more accurate screening and surveillance program by identifying higher-risk patients on a molecular basis. It could also provide justification for more definitive follow up of patients who have molecular but not yet all the pathological or clinical features associated with malignancy. 
         [0016]    Predicting Treatment Response 
         [0017]    Information about how a cancer develops through molecular events could allow a clinician to predict more accurately how such a cancer is likely to respond to specific chemotherapeutic agents. In this way, a regimen based on knowledge of the tumor&#39;s chemosensitivity could be rationally designed. Studies have shown that hypermethylation of the MGMT promoter in glioma patients is indicative of a good response to therapy, greater overall survival and a longer time to progression. 
         [0018]    There is a continuing need in the art for new diagnostic markers and therapeutic targets for cancer to improve management of patient care. 
       SUMMARY OF THE INVENTION 
       [0019]    According to a first embodiment of the invention a method is provided for identifying a cell as neoplastic or predisposed to neoplasia. Epigenetic silencing of at least one gene listed in Table 5 is detected in a test cell. The test cell is identified as neoplastic or predisposed to neoplasia based on the detection of epigenetic silencing. 
         [0020]    In another embodiment of the invention a method is provided for reducing or inhibiting neoplastic growth of a cell which exhibits epigenetic silenced transcription of at least one gene associated with a cancer. The cell may be a cervical, prostate, lung, breast, or colon cell. Expression of a polypeptide encoded by the epigenetic silenced gene is restored in the cell by contacting the cell with a CpG dinucleotide demethylating agent or with an agent that changes the histone acetylation status of cellular DNA or any other treatment affecting epigenetic mechanisms present in cells. The gene is selected from those listed in Table 5. Unregulated growth of the cell is thereby reduced or inhibited. If the cell is a breast or lung cell, the gene may or may not be APC. Expression of the gene is tested in the cell to monitor response to the demethylating or other epigenetic affecting agent. 
         [0021]    Another aspect of the invention is a method of reducing or inhibiting neoplastic growth of a cell which exhibits epigenetic silenced transcription of at least one gene associated with a cancer. The cell may be a cervical prostate, lung, breast, or colon cell. A polynucleotide encoding a polypeptide is introduced into a cell which exhibits epigenetic silenced transcription of at least one gene listed in Table 5. The polypeptide is encoded by the epigenetic-silenced gene. The polypeptide is thereby expressed in the cell thereby restoring expression of the polypeptide in the cell. If the cell is a breast or lung cell, the gene may or may not be APC. 
         [0022]    Still another aspect of the invention is a method of treating a cancer patient. The cancer may be a cervical prostate, lung, breast, or colon cell. A demethylating agent is administered to the patient in sufficient amounts to restore expression of a tumor-associated methylation-silenced gene selected from those listed in Table 5 in the patient&#39;s tumor. If the cancer is a breast or lung cancer, the gene may or may not be APC. Expression of the gene is tested in cancer cells of the patient to monitor response to the demethylating agent. 
         [0023]    An additional embodiment of the invention provides a method of treating a cancer patient. The cancer may be a cervical, prostate, lung, breast, or colon cancer. A polynucleotide encoding a polypeptide is administered to the patient. The polypeptide is encoded by a gene listed in Table 5. The polypeptide is expressed in the patient&#39;s tumor thereby restoring expression of the polypeptide in the tumor. If the cancer is a breast or lung cancer, the gene may or may not be APC. 
         [0024]    Yet another embodiment of the invention is a method for selecting a therapeutic strategy for treating a cancer patient. A gene selected from those listed in Table 5 whose expression in cancer cells of the patient is reactivated by a demethylating agent is identified. A therapeutic agent which reactivates expression of the gene is selected for treating the cancer patient. If the cancer cells are breast or lung cells, the gene may or may not be APC. 
         [0025]    A further embodiment of the invention is a kit for assessing methylation in a cell sample. The kit comprises certain components in a package. One component is a reagent that (a) modifies methylated cytosine residues but not non-methylated cytosine residues, or that (b) modifies non-methylated cytosine residues but not methylated cytosine residues. A second component is a pair of oligonucleotide primers that specifically hybridizes under amplification conditions to a region of a gene selected from those listed in Table 5. The region is within about 1 kb of said gene&#39;s transcription start site. 
         [0026]    These and other embodiments which will be apparent to those of skill in the art upon reading the specification provide the art with tools and methods for detection, diagnosis, therapy, and drug selection pertaining to neoplastic cells and cancers. 
       BRIEF DESCRIPTION OF THE TABLES 
       [0027]    Table 1. Squamous lung cancer reactivated genes 
         [0028]    Table 2. Adenocarcinoma lung cancer reactivated genes 
         [0029]    Table 3. All lung cancer reactivated genes 
         [0030]    Table 4. Prostate cancer reactivated genes 
         [0031]    Table 5. All cancer reactivated genes 
         [0032]    Table 6. Breast cancer reactivated genes 
         [0033]    Table 7. Colorectal cancer reactivated genes 
         [0034]    Table 8. Cervical cancer reactivated genes 
         [0035]    Table 9. Combinations of two and three squamous lung cancer reactivated genes (on CD.) 
         [0036]    Table 10. Combinations of two and three adenocarcinoma lung cancer reactivated genes (on CD) 
         [0037]    Table 11. Combinations of two and three prostate cancer reactivated genes (on CD) 
         [0038]    Table 12. Combinations of two and three breast cancer reactivated genes (on CD) 
         [0039]    Table 13. Combinations of two and three colorectal cancer reactivated genes (on CD) 
         [0040]    Table 14. Combinations of two and three cervical cancer reactivated genes (on CD) 
         [0041]    Table 15. Correlation of transcript sequence to encoded protein sequence; also provides the order that the genes and proteins are listed in the sequence listing 
         [0042]    Table 16. BSP results for cervical cancer tissues. 
         [0043]    Table 17. Correlation of transcript accession number to gene/protein name 
         [0044]    Table 18. Results for lung cancer tissues. 
         [0045]    Table 19. Results for breast cancer tissues 
         [0046]    Table 20. Results for colon cancer tissues. 
     
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
         [0047]      FIG. 1A-1B : Methylation specific PCR (MSP) for CCNA1 ( FIG. 1A ) and NPTX1 ( FIG. 1B ) 
           [0048]      FIG. 2A : Methylation specific PCR (MSP) for CEBPC and PODXL 
       
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
       [0049]    The inventors have discovered a set of genes whose transcription is epigenetically silenced in cancers. All of the identified genes are shown in Table 5. Subsets which are associated with particular cancers are shown in Tables 1-4 and 6-8. 
         [0050]    Epigenetic silencing of a gene can be determined by any method known in the art. One method is to determine that a gene which is expressed in normal cells is less expressed or not expressed in tumor cells. This method does not, on its own, however, indicate that the silencing is epigenetic, as the mechanism of the silencing could be genetic, for example, by somatic mutation. One method to determine that the silencing is epigenetic is to treat with a reagent, such as DAC (5′-deazacytidine), or with a reagent which changes the histone acetylation status of cellular DNA or any other treatment affecting epigenetic mechanisms present in cells, and observe that the silencing is reversed, i.e., that the expression of the gene is reactivated or restored. Another means to determine epigenetic silencing is to determine the presence of methylated CpG dinucleotide motifs in the silenced gene. Typically these reside near the transcription start site, for example, within about 1 kbp, within about 750 bp, or within about 500 bp. 
         [0051]    Expression of a gene can be assessed using any means known in the art. Either mRNA or protein can be measured. Methods employing hybridization to nucleic acid probes can be employed for measuring specific mRNAs. Such methods include using nucleic acid probe arrays (microarray technology), in situ hybridization, and using Northern blots. Messenger RNA can also be assessed using amplification techniques, such as RT-PCR. Advances in genomic technologies now permit the simultaneous analysis of thousands of genes, although many are based on the same concept of specific probe-target hybridization. Sequencing-based methods are an alternative; these methods started with the use of expressed sequence tags (ESTs), and now include methods based on short tags, such as serial analysis of gene expression (SAGE) and massively parallel signature sequencing (MPSS). Differential display techniques provide yet another means of analyzing gene expression; this family of techniques is based on random amplification of cDNA fragments generated by restriction digestion, and bands that differ between two tissues identify cDNAs of interest. Specific proteins can be assessed using any convenient method including immunoassays and immuno-cytochemistry but are not limited to that. Most such methods will employ antibodies which are specific for the particular protein or protein fragments. The sequences of the mRNA (cDNA) and proteins of the markers of the present invention are provided in the sequence listing. The sequences are provided in the order of increasing accession numbers as shown in Table 15. 
         [0052]    Methylation-sensitive restriction endonucleases can be used to detect methylated CpG dinucleotide motifs. Such endonucleases may either preferentially cleave methylated recognition sites relative to non-methylated recognition sites or preferentially cleave non-methylated relative to methylated recognition sites. Examples of the former are Acc III, Ban I, BstN I, Msp I, and Xma I. Examples of the latter are Acc II, Ava I, BssH II, BstU I, Hpa II, and Not I. Alternatively, chemical reagents can be used which selectively modify either the methylated or non-methylated form of CpG dinucleotide motifs. 
         [0053]    Modified products can be detected directly, or after a further reaction which creates products which are easily distinguishable. Means which detect altered size and/or charge can be used to detect modified products, including but not limited to electrophoresis, chromatography, and mass spectrometry. Examples of such chemical reagents for selective modification include hydrazine and bisulfite ions. Hydrazine-modified DNA can be treated with piperidine to cleave it. Bisulfite ion-treated DNA can be treated with alkali. 
         [0054]    A variety of amplification techniques may be used in a reaction for creating distinguishable products. Some of these techniques employ PCR. Other suitable amplification methods include the ligase chain reaction (LCR) (Barringer et al, 1990), transcription amplification (Kwoh et al. 1989; WO88/10315), selective amplification of target polynucleotide sequences (U.S. Pat. No. 6,410,276), consensus sequence primed polymerase chain reaction (U.S. Pat. No. 4,437,975), arbitrarily primed polymerase chain reaction (WO90/06995), nucleic acid based sequence amplification (NASBA) (U.S. Pat. Nos. 5,409,818; 5,554,517; 6,063,603), nick displacement amplification (WO2004/067726). 
         [0055]    Sequence variation that reflects the methylation status at CpG dinucleotides in the original genomic DNA offers two approaches to PCR primer design. In the first approach, the primers do not themselves do not “cover” or hybridize to any potential sites of DNA methylation; sequence variation at sites of differential methylation are located between the two primers. Such primers are used in bisulphite genomic sequencing, COBRA, Ms-SNuPE. In the second approach, the primers are designed to anneal specifically with either the methylated or unmethylated version of the converted sequence. If there is a sufficient region of complementarity, e.g., 12, 15, 18, or 20 nucleotides, to the target, then the primer may also contain additional nucleotide residues that do not interfere with hybridization but may be useful for other manipulations. Exemplary of such other residues may be sites for restriction endonuclease cleavage, for ligand binding or for factor binding or linkers or repeats. The oligonucleotide primers may or may not be such that they are specific for modified methylated residues 
         [0056]    One way to distinguish between modified and unmodified DNA is to hybridize oligonucleotide primers which specifically bind to one form or the other of the DNA. After hybridization, an amplification reaction can be performed and amplification products assayed. The presence of an amplification product indicates that a sample hybridized to the primer. The specificity of the primer indicates whether the DNA had been modified or not, which in turn indicates whether the DNA had been methylated or not. For example, bisulfite ions modify non-methylated cytosine bases, changing them to uracil bases. Uracil bases hybridize to adenine bases under hybridization conditions. Thus an oligonucleotide primer which comprises adenine bases in place of guanine bases would hybridize to the bisulfite-modified DNA, whereas an oligonucleotide primer containing the guanine bases would hybridize to the non-modified (methylated) cytosine residues in the DNA. Amplification using a DNA polymerase and a second primer yield amplification products which can be readily observed. Such a method is termed MSP (Methylation Specific PCR; U.S. Pat. Nos. 5,786,146; 6,017,704; 6,200,756). The amplification products can be optionally hybridized to specific oligonucleotide probes which may also be specific for certain products. Alternatively, oligonucleotide probes can be used which will hybridize to amplification products from both modified and nonmodified DNA. 
         [0057]    Another way to distinguish between modified and nonmodified DNA is to use oligonucleotide probes which may also be specific for certain products. Such probes can be hybridized directly to modified DNA or to amplification products of modified DNA. Oligonucleotide probes can be labeled using any detection system known in the art. These include but are not limited to fluorescent moieties, radioisotope labeled moieties, bioluminescent moieties, luminescent moieties, chemiluminescent moieties, enzymes, substrates, receptors, or ligands. 
         [0058]    Still another way for the identification of methylated CpG dinucleotides utilizes the ability of the MBD domain of the McCP2 protein to selectively bind to methylated DNA sequences (Cross et al, 1994; Shiraishi et al, 1999). Restriction enconuclease digested genomic DNA is loaded onto expressed His-tagged methyl-CpG binding domain that is immobilized to a solid matrix and used for preparative column chromatography to isolate highly methylated DNA sequences. 
         [0059]    Real time chemistry allow for the detection of PCR amplification during the early phases of the reactions, and makes quantitation of DNA and RNA easier and more precise. A few variations of the real-time PCR are known. They include the TaqMan system and Molecular Beacon system which have separate probes labeled with a fluorophore and a fuorescence quencher. In the Scorpion system the labeled probe in the form of a hairpin structure is linked to the primer. 
         [0060]    DNA methylation analysis has been performed successfully with a number of techniques which include the MALDI-TOFF, MassARRAY, MethyLight, Quantitative analysis of ethylated alleles (QAMA), enzymatic regional methylation assay (ERMA), HeavyMethyl, QBSUPT, MS-SNuPE, MethylQuant, Quantitative PCR sequencing, Oligonucleotide-based microarray, systems. 
         [0061]    The number of genes whose silencing is tested and/or detected can vary: one, two, three, four, five, or more genes can be tested and/or detected. In some cases at least two genes are selected from one table selected from Tables 1-4 and 6-8. In other embodiments at least three genes are selected from one table selected from Tables 1-4 and 6-8. 
         [0062]    If one or at least two genes are being tested and the cell is a prostate cell, at least one gene can be selected from the group consisting of CD3D, APOC1, NBL1, ING4, LEF1, CENTD3, MGC15396, FKBP4, PLTP, TFAP2A, ATXN1, BMP2, ENPEP, MCAM, SSBP2, PDLIM3 and NDP. More particularly, at least one gene can be selected from the group consisting of BMP2, ENPEP, MCAM, SSBP2, and NDP. 
         [0063]    If one or at least two genes are being tested and the cell is a lung cell, at least one gene can be selected from the group consisting of PHKA2, CBR3, CAMK4, HOXB5, ZNF198, RGS4, RBM15B, PDLIM3, PAK3, PIGH, TUBB4, and NISCH. More particularly, at least one gene can be selected from the group consisting of PAK3, PIGH, TUBB4, and NISCH. 
         [0064]    If one or at least two genes are being tested and the cell is a breast cell, at least one gene can be selected from the group consisting of BACH1, CKMT, GALE, HMG20B, KRT14, OGDHL, PON2, SESN1, KIF1A (kinesin family member 1A) PDLIM3 and MAL (T cell proliferation protein). More particularly, at least one gene can be elected from the group consisting of KIF1A (kinesin family member 1A) and MAL (T cell proliferation protein). 
         [0065]    If one or at least two genes are being tested and the cell is a colon cell, at least one gene can be selected from the group consisting of B4GALT1, C10orf119, C10orf13, CBR1, COPS4, COVA1, CSRP1, DARS, DNAJC10, FKBP14, FN3KRP, GANAB, HUS1, KLF11, MRPLA, MYLK, NELF, NETO2, PAPSS2, RBMS2, RHOB, SECTM1, SIRT2, SIRT7, SLC35D1, SLC9A3R1, TTRAP, TUBG2, FLJ20277, MYBL2, GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. More particularly, at least one gene can be selected from the group consisting of GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. 
         [0066]    If one or at least two genes are being tested and the cell is a cervical cancer cell, at least one gene can be selected from the group consisting of PDCD4, TFPI2, ARMC7, TRM-HUMAN, OGDHL, PTGS2, CDK6, GPR39, HMGN2, C130RF18, ASMTL, DLL4, NP-659450.1, NP-078820.1, CLU, HPCA, PLCG2, RALY, GNB4, CCNA1 NPTX1 and C90RF19. Particularly the at least one gene can be selected from the group consisting of TFPI2, ARMC7, TRM_HUMAN, OGDHL, PTGS2, GPR39, C13ORF18, ASMTL, CCNA1, NPTX1 and DLL4. 
         [0067]    Testing can be performed diagnostically or in conjunction with a therapeutic regimen. Testing can be used to monitor efficacy of a therapeutic regimen, whether a chemotherapeutic agent or a biological agent, such as a polynucleotide. 
         [0068]    Test cells for diagnostic, prognostic, or personalized medicine uses can be obtained from surgical samples, such as biopsies or fine needle aspirates, from paraffin embedded colon, rectum, breast, ovary, prostate, kidney, lung, brain on other organ tissues, from a body fluid such as bone marrow, blood, serum, lymph, cerebrospinal fluid, saliva, sputum, bronchial-lavage fluid, ductal fluids stool, urine, lymph nodes or semen. Such sources are not meant to be exhaustive, but rather exemplary. A test cell obtainable from such samples or fluids includes detached tumor cells or free nucleic acids that are released from dead tumor cells. Nucleic acids include RNA, genomic DNA, mitochondrial DNA, single or double stranded, and protein-associated nucleic acids. Any nucleic acid specimen in purified or non-purified form obtained from such test cell can be utilized as the starting nucleic acid or acids. 
         [0069]    Demethylating agents can be contacted with cells in vitro or in vivo for the purpose of restoring normal gene expression to the cell. Suitable demethylating agents include, but are not limited to 5-aza-2′-deoxycytidine, 5-aza-cytidine, Zebularine, procaine, and L-ethionine. This reaction may be used for diagnosis, for determining predisposition, and for determining suitable therapeutic regimes. If the demethylating agent is used for treating colon, breast, lung, or prostate cancers, expression or methylation can be tested of a gene selected from the group consisting of CD3D, APOC1, NBL1, ING4, LEF1, CENTD3, MGC15396, FKBP4, PLTP, TFAP2A, ATXN1, BMP2, ENPEP, MCAM, SSBP2, PDLIM3, NDP, PHKA2, CBR3, CAMK4, HOXB5, ZNF198, RGS4, RBM15B, PDLIM3, PAK3, PIGH, TUBB4, NISCH, BACH1, CKMT, GALE, HMG20B, KRT14, OGDHL, PON2, SESN1, KIF1A (kinesin family member 1A) PDLIM3, MAL (T cell proliferation protein) B4GALT1, C10orf119, C10orf13, CBR1, COPS4, COVA1, CSRP1, DARS, DNAJC10, FKBP14, FN3KRP, GANAB, HUS1, KLF11, MRPL4, MYLK, NELF, NETO2, PAPSS2, RBMS2, RHOB, SECTM1, SIRT2, SIRT7, SLC35D1, SLC9A3R1, TTRAP, TUBG2, FLJ20277, MYBL2, GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. If the cell is a prostate cell, the gene can be selected from the group consisting of BMP2, ENPEP, MCAM, SSBP2, and NDP. If the cell is a lung cell, the gene can be selected from the group consisting of PAK3, PIGH, TUBB4, and NISCH. If the cell is a breast cell, the gene can be selected from the group consisting of KIF1A (kinesin family member 1A) and MAL (T cell proliferation protein). If the cell is a colon cell, the gene can be selected from the group consisting of GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. If the cell is a cervical cancer cell, at least one gene can be selected from the group consisting of PDCD4, TFPI2, ARMC7, TRM-HUMAN, OGDHL, PTGS2, CDK6, GPR39, HMGN2, C130RF18, ASMTL, DLL4, NP-659450.1, NP-078820.1, CLU, HPCA, PLCG2, RALY, GNB4, CCNA1 NPTX1 and C90RF19. Particularly the at least one gene can be selected from the group consisting of TFPI2, ARMC7, TRM_HUMAN, OGDHL, PTGS2, GPR39, C130RF18, ASMTL, CCNA1, NPTX1 and DLL4. 
         [0070]    An alternative way to restore epigenetically silenced gene expression is to introduce a non-methylated polynucleotide into a cell, so that it will be expressed in the cell. Various gene therapy vectors and vehicles are known in the art and any can be used as is suitable for a particular situation. Certain vectors are suitable for short term expression and certain vectors are suitable for prolonged expression. Certain vectors are trophic for certain organs and these can be used as is appropriate in the particular situation. Vectors may be viral or non-viral. The polynucleotide can, but need not, be contained in a vector, for example, a viral vector, and can be formulated, for example, in a matrix such as a liposome, microbubbles. The polynucleotide can be introduced into a cell by administering the polynucleotide to the subject such that it contacts the cell and is taken up by the cell and the encoded polypeptide expressed. Suitable polynucleotides are provided in the sequence listing SEQ ID NO: 1-210. Polynucleotides encoding the polypeptides shown in SEQ ID NO: 211-420 can also be used. Preferably the specific polynucleotide will be one which the patient has been tested for and been found to carry a silenced version. The polynucleotides for treating colon, breast, lung, or prostate cancers will typically encode a gene selected from the group consisting of CD3D, APOC1, NBL1, ING4, LEF1, CENTD3, MGC15396, FKBP4, PLTP, TFAP2A, ATXN1, BMP2, ENPEP, MCAM, SSBP2, PDLIM3, NDP, PHKA2, CBR3, CAMK4, HOXB5, ZNF198, RGS4, RBM15B, PDLIM3, PAK3, PIGH, TUBB4, NISCH, BACH1, CKMT, GALE, HMG20B, KRT14, OGDHL, PON2, SESN1, KIF1A (kinesin family member 1A) PDLIM3, MAL (T cell proliferation protein) B4GALT1, C10orf119, C10orf13, CBR1, COPS4, COVA1, CSRP1, DARS, DNAJC10, FKBP14, FN3KRP, GANAB, HUS1, KLF11, MRPL4, MYLK, NELF, NETO2, PAPSS2, RBMS2, RHOB, SECTM1, SIRT2, SIRT7, SLC35D1, SLC9A3R1, TTRAP, TUBG2, FLJ20277, MYBL2, GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. If the cell is a prostate cell, the gene can be selected from the group consisting of BMP2, ENPEP, MCAM, SSBP2, and NDP. If the cell is a lung cell, the gene can be selected from the group consisting of PAK3, PIGH, TUBB4, and NISCH. If the cell is a breast cell, the gene can be selected from the group consisting of KIF1A (kinesin family member 1A) and MAL (T cell proliferation protein). If the cell is a colon cell, the gene can be selected from the group consisting of GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. If the cell is a cervical cancer cell, at least one gene can be selected from the group consisting of PDCD4, TFPI2, ARMC7, TRM-HUMAN, OGDHL, PTGS2, CDK6, GPR39, HMGN2, C130RF18, ASMTL, DLL4, NP-659450.1, NP-078820.1, CLU, HPCA, PLCG2, RALY, GNB4, CCNA1 NPTX1 and C90RF19. Particularly the at least one gene can be selected from the group consisting of TFPI2, ARMC7, TRM_HUMAN, OGDHL, PTGS2, GPR39, C13ORF18, ASMTL, CCNA1, NPTX1 and DLL4. 
         [0071]    Cells exhibiting methylation silenced gene expression generally are contacted with the demethylating agent in vivo by administering the agent to a subject. Where convenient, the demethylating agent can be administered using, for example, a catheterization procedure, at or near the site of the cells exhibiting unregulated growth in the subject, or into a blood vessel in which the blood is flowing to the site of the cells. Similarly, where an organ, or portion thereof, to be treated can be isolated by a shunt procedure, the agent can be administered via the shunt, thus substantially providing the agent to the site containing the cells. The agent also can be administered systemically or via other routes known in the art. 
         [0072]    The polynucleotide can include, in addition to polypeptide coding sequence, operatively linked transcriptional regulatory elements, translational regulatory elements, and the like, and can be in the form of a naked DNA molecule, which can be contained in a vector, or can be formulated in a matrix such as a liposome or microbubbles that facilitates entry of the polynucleotide into the particular cell. The term “operatively linked” refers to two or more molecules that are positioned with respect to each other such that they act as a single unit and effect a function attributable to one or both molecules or a combination thereof. A polynucleotide sequence encoding a desired polypeptide can be operatively linked to a regulatory element, in which case the regulatory element confers its regulatory effect on the polynucleotide similar to the way in which the regulatory element would affect a polynucleotide sequence with which it normally is associated with in a cell. 
         [0073]    The polynucleotide encoding the desired polypeptide to be administered to a mammal or a human or to be contacted with a cell may contain a promoter sequence, which can provide constitutive or, if desired, inducible or tissue specific or developmental stage specific expression of the polynucleotide, a poly-A recognition sequence, and a ribosome recognition site or internal ribosome entry site, or other regulatory elements such as an enhancer, which can be tissue specific. The vector also may contain elements required for replication in a prokaryotic or eukaryotic host system or both, as desired. Such vectors, which include plasmid vectors and viral vectors such as bacteriophage, baculovirus, retrovirus, lentivirus, adenovirus, vaccinia virus, semliki forest virus and adeno-associated virus vectors, are well known and can be purchased from a commercial source (Promega, Madison Wis.; Stratagene, La Jolla Calif.; GIBCO/BRL, Gaithersburg Md.) or can be constructed by one skilled in the art (see, for example, Meth. Enzymol., Vol. 185, Goeddel, ed. (Academic Press, Inc., 1990); Jolly, Canc. Gene Ther. 1:51-64, 1994; Flotte, S. Bioenerg. Biomemb. 25:37-42, 1993; Kirshenbaum et al., J. Clin. Invest. 92:381-387, 1993; each of which is incorporated herein by reference). 
         [0074]    A tetracycline (tet) inducible promoter can be used for driving expression of a polynucleotide encoding a desired polypeptide. Upon administration of tetracycline, or a tetracycline analog, to a subject containing a polynucleotide operatively linked to a tet inducible promoter, expression of the encoded polypeptide is induced. The polynucleotide alternatively can be operatively linked to tissue specific regulatory element, for example, a liver cell specific regulatory element such as an α.-fetoprotein promoter (Kanai et al., Cancer Res. 57:461-465, 1997; He et al., J. Exp. Clin. Cancer Res. 19:183-187, 2000) or an albumin promoter (Power et al., Biochem. Biophys. Res. Comm. 203:1447-1456, 1994; Kuriyama et al., Int. J. Cancer 71:470-475, 1997); a muscle cell specific regulatory element such as a myoglobin promoter (Devlin et al., J. Biol. Chem. 264:13896-13901, 1989; Yan et al., J. Biol. Chem. 276:17361-17366, 2001); a prostate cell specific regulatory element such as the PSA promoter (Schuur et al., J. Biol. Chem. 271:7043-7051, 1996; Latham et al., Cancer Res. 60:334-341, 2000); a pancreatic cell specific regulatory element such as the elastase promoter (Ornitz et al., Nature 313:600-602, 1985; Swift et al., Genes Devel. 3:687-696, 1989); a leukocyte specific regulatory element such as the leukosialin (CD43) promoter (Shelley et al., Biochem. J. 270:569-576, 1990; Kudo and Fukuda, J. Biol. Chem. 270:13298-13302, 1995); or the like, such that expression of the polypeptide is restricted to particular cell in an individual, or to particular cells in a mixed population of cells in culture, for example, an organ culture. Regulatory elements, including tissue specific regulatory elements, many of which are commercially available, are well known in the art (see, for example, InvivoGen; San Diego Calif.). 
         [0075]    Viral expression vectors can be used for introducing a polynucleotide into a cell, particularly a cell in a subject. Viral vectors provide the advantage that they can infect host cells with relatively high efficiency and can infect specific cell types. For example, a polynucleotide encoding a desired polypeptide can be cloned into a baculovirus vector, which then can be used to infect an insect host cell, thereby providing a means to produce large amounts of the encoded polypeptide. Viral vectors have been developed for use in particular host systems, particularly mammalian systems and include, for example, retroviral vectors, other lentivirus vectors such as those based on the human immunodeficiency virus (HIV), adenovirus vectors, adeno-associated virus vectors, herpesvirus vectors, hepatitis virus vectors, vaccinia virus vectors, and the like (see Miller and Rosman, BioTechniques 7:980-990, 1992; Anderson et al., Nature 392:25-30 Suppl., 1998; Verna and Somia, Nature 389:239-242, 1997; Wilson, New Engl. J. Med. 334:1185-1187 (1996), each of which is incorporated herein by reference). 
         [0076]    A polynucleotide, which can optionally be contained in a vector, can be introduced into a cell by any of a variety of methods known in the art (Sambrook et al., supra, 1989; Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1987, and supplements through 1995), each of which is incorporated herein by reference). Such methods include, for example, transfection, lipofection, microinjection, electroporation and, with viral vectors, infection; and can include the use of liposomes, microemulsions or the like, which can facilitate introduction of the polynucleotide into the cell and can protect the polynucleotide from degradation prior to its introduction into the cell. A particularly useful method comprises incorporating the polynucleotide into microbubbles, which can be injected into the circulation. An ultrasound source can be positioned such that ultrasound is transmitted to the tumor, wherein circulating microbubbles containing the polynucleotide are disrupted at the site of the tumor due to the ultrasound, thus providing the polynucleotide at the site of the cancer. The selection of a particular method will depend, for example, on the cell into which the polynucleotide is to be introduced, as well as whether the cell is in culture or in situ in a body. 
         [0077]    Introduction of a polynucleotide into a cell by infection with a viral vector can efficiently introduce the nucleic acid molecule into a cell. Moreover, viruses are very specialized and can be selected as vectors based on an ability to infect and propagate in one or a few specific cell types. Thus, their natural specificity can be used to target the nucleic acid molecule contained in the vector to specific cell types. A vector based on an HIV can be used to infect T cells, a vector based on an adenovirus can be used, for example, to infect respiratory epithelial cells, a vector based on a herpesvirus can be used to infect neuronal cells, and the like. Other vectors, such as adeno-associated viruses can have greater host cell range and, therefore, can be used to infect various cell types, although viral or non-viral vectors also can be modified with specific receptors or ligands to alter target specificity through receptor mediated events. A polynucleotide of the invention, or a vector containing the polynucleotide can be contained in a cell, for example, a host cell, which allows propagation of a vector containing the polynucleotide, or a helper cell, which allows packaging of a viral vector containing the polynucleotide. The polynucleotide can be transiently contained in the cell, or can be stably maintained due, for example, to integration into the cell genome. 
         [0078]    A polypeptide according to any of SEQ ID NO: 211-420 can be administered directly to the site of a cell exhibiting unregulated growth in the subject. The polypeptide can be produced and isolated, and formulated as desired, using methods as disclosed herein, and can be contacted with the cell such that the polypeptide can cross the cell membrane of the target cells. The polypeptide may be provided as part of a fusion protein, which includes a peptide or polypeptide component that facilitates transport across cell membranes. For example, a human immunodeficiency virus (HIV) TAT protein transduction domain or a nuclear localization domain may be fused to the marker of interest. The administered polypeptide can be formulated in a matrix that facilitates entry of the polypeptide into a cell. 
         [0079]    An agent such as a demethylating agent, a polynucleotide, or a polypeptide is typically formulated in a composition suitable for administration to the subject. Thus, the invention provides compositions containing an agent that is useful for restoring regulated growth to a cell exhibiting unregulated growth due to methylation silenced transcription of one or more genes. The agents are useful as medicaments for treating a subject suffering from a pathological condition associated with such unregulated growth. Such medicaments generally include a carrier. Acceptable carriers are well known in the art and include, for example, aqueous solutions such as water or physiologically buffered saline or other solvents or vehicles such as glycols, glycerol, oils such as olive oil or injectable organic esters. An acceptable carrier can contain physiologically acceptable compounds that act, for example, to stabilize or to increase the absorption of the conjugate. Such physiologically acceptable compounds include, for example, carbohydrates, such as glucose, sucrose or dextrans, antioxidants, such as ascorbic acid or glutathione, chelating agents, low molecular weight proteins or other stabilizers or excipients. One skilled in the art would know or readily be able to determine an acceptable carrier, including a physiologically acceptable compound. The nature of the carrier depends on the physico-chemical characteristics of the therapeutic agent and on the route of administration of the composition. Administration of therapeutic agents or medicaments can be by the oral route or parenterally such as intravenously, intramuscularly, subcutaneously, transdermally, intranasally, intrabronchially, vaginally, rectally, intratunorally, or other such method known in the art. The pharmaceutical composition also can contain one more additional therapeutic agents. 
         [0080]    The therapeutic agents can be incorporated within an encapsulating material such as into an oil-in-water emulsion, a microemulsion, micelle, mixed micelle, liposome, microsphere, microbubbles or other polymer matrix (see, for example, Gregoriadis, Liposome Technology, Vol. 1 (CRC Press, Boca Raton, Fla. 1984); Fraley, et al., Trends Biochem. Sci., 6:77 (1981), each of which is incorporated herein by reference). Liposomes, for example, which consist of phospholipids or other lipids, are nontoxic, physiologically acceptable and metabolizable carriers that are relatively simple to make and administer. “Stealth” liposomes (see, for example, U.S. Pat. Nos. 5,882,679; 5,395,619; and 5,225,212, each of which is incorporated herein by reference) are an example of such encapsulating materials particularly useful for preparing a composition useful in a method of the invention, and other “masked” liposomes similarly can be used, such liposomes extending the time that the therapeutic agent remain in the circulation. Cationic liposomes, for example, also can be modified with specific receptors or ligands (Morishita et al., J. Clin. Invest., 91:2580-2585 (1993), which is incorporated herein by reference). In addition, a polynucleotide agent can be introduced into a cell using, for example, adenovirus-polylysine DNA complexes (see, for example, Michael et al., J. Biol. Chem. 268:6866-6869 (1993), which is incorporated herein by reference). 
         [0081]    The route of administration of the composition containing the therapeutic agent will depend, in part, on the chemical structure of the molecule. Polypeptides and polynucleotides, for example, are not efficiently delivered orally because they can be degraded in the digestive tract. However, methods for chemically modifying polypeptides, for example, to render them less susceptible to degradation by endogenous proteases or more absorbable through the alimentary tract may be used (see, for example, Blondelle et al., supra, 1995; Ecker and Crook, supra, 1995). 
         [0082]    The total amount of an agent to be administered in practicing a method of the invention can be administered to a subject as a single dose, either as a bolus or by infusion over a relatively short period of time, or can be administered using a fractionated treatment protocol, in which multiple doses are administered over a prolonged period of time. One skilled in the art would know that the amount of the composition to treat a pathologic condition in a subject depends on many factors including the age and general health of the subject as well as the route of administration and the number of treatments to be administered. In view of these factors, the skilled artisan would adjust the particular dose as necessary. In general, the formulation of the composition and the routes and frequency of administration are determined, initially, using Phase I and Phase II clinical trials. 
         [0083]    The composition can be formulated for oral formulation, such as a tablet, or a solution or suspension form; or can comprise an admixture with an organic or inorganic carrier or excipient suitable for enteral or parenteral applications, and can be compounded, for example, with the usual non-toxic, pharmaceutically acceptable carriers for tablets, pellets, capsules, suppositories, solutions, emulsions, suspensions, or other form suitable for use. The carriers, in addition to those disclosed above, can include glucose, lactose, mannose, gum acacia, gelatin, mannitol, starch paste, magnesium trisilicate, talc, corn starch, keratin, colloidal silica, potato starch, urea, medium chain length triglycerides, dextrans, and other carriers suitable for use in manufacturing preparations, in solid, semisolid, or liquid form. In addition auxiliary, stabilizing, thickening or coloring agents and perfumes can be used, for example a stabilizing dry agent such as triulose (see, for example, U.S. Pat. No. 5,314,695). 
         [0084]    Although accuracy and sensitivity may be achieved by using a combination of markers, such as 5 or 6 markers, practical considerations may dictate use of smaller combinations. Any combination of markers for a specific cancer may be used which comprises 2, 3, 4, or 5 markers. Each of the combinations for two and three markers are listed in attached Tables found on CD-ROM. Other combinations of four or five markers can be readily envisioned given the specific disclosures of individual markers provided herein. 
         [0085]    The level of methylation of the differentially methylated GpG islands can provide a variety of information a about the disease or cancer. It can be used to diagnose a disease or cancer in the individual. Alternatively, it can be used to predict the course of the disease or cancer in the individual or to predict the suspectibility to disease or cancer or to stage the progression of the disease or cancer in the individual. Otherwise, it can help to predict the likelihood of overall survival or predict the likelihood of reoccurrence of disease or cancer and to determine the effectiveness of a treatment course undergone by the individual. Increase or decrease of methylation levels in comparison with reference level and alterations in the increase/decrease when detected provide useful prognostic and diagnostic value. 
         [0086]    The prognostic methods can be used to identify surgically treated patients likely to experience cancer reoccurrence. Such patients can be offered additional therapeutic options, including pre-operative or post-operative options such as chemotherapy, radiation, biological modifiers, or other therapies. 
         [0087]    A therapeutic strategy for treating a prostate, lung, breast, or colon cancer patient can be selected based on reactivation of epigenetically silenced genes. First a gene selected from those listed in Table 5 is identified whose expression in cancer cells of the patient is reactivated by a demethylating agent. Then a therapeutic agent is selected which reactivates expression of the gene. If the cancer cells are breast or lung cells, the gene is not APC. If the cell is a prostate cell, a lung cell, a breast cell or a colon cell, the gene can be selected from the group consisting of CD3D, APOC1, NBL1, ING4, LEF1, CENTD3, MGC15396, FKBP4, PLTP, TFAP2A, ATXN1, BMP2, ENPEP, MCAM, SSBP2, PDLIM3, NDP, PHKA2, CBR3, CAMK4, HOXB5, ZNF198, RGS4, RBM15B, PDLIM3, PAK3, PIGH, TUBB4, NISCH, BACH1, CKMT, GALE, HMG20B, KRT14, OGDHL, PON2, SESN1, KIF1A (kinesin family member 1A) PDLIM3, MAL (T cell proliferation protein) B4GALT1, C10orf119, C10orf13, CBR1, COPS4, COVA1, CSRP1, DARS, DNAJC10, FKBP14, FN3KRP, GANAB, HUS1, KLF11, MRPL4, MYLK, NELF, NETO2, PAPSS2, RBMS2, RHOB, SECTM1, SIRT2, SIRT7, SLC35D1, SLC9A3R1, TTRAP, TUBG2, FLJ20277, MYBL2, GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. More particularly, the gene can be selected from the group consisting of BMP2, ENPEP, MCAM, SSBP2, NDP, PAK3, PIGH, TUBB4, and NISCH. KIF1A (kinesin family member 1A), MAL (T cell proliferation protein), GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. If the cancer is prostate cancer, the gene can be selected from the group consisting of BMP2, ENPEP, MCAM, SSBP2, and NDP. If the cancer is lung cancer, the gene can be selected from the group consisting of PAK3, PIGH, TUBB4, and NISCH. If the cancer is breast cancer, the gene can be selected from the group consisting of KIF1A (kinesin family member 1A) and MAL (T cell proliferation protein). If the cancer is colon cancer, the gene can be selected from the group consisting of GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3, and 1UBE21. If the cell is a cervical cancer cell, at least one gene can be selected from the group consisting of PDCD4, TFPI2, ARMC7, TRM-HUMAN, OGDHL, PTGS2, CDK6, GPR39, HMGN2, C130RF18, ASMTL, DLL4, NP-659450.1, NP-078820.1, CLU, HPCA, PLCG2, RALY, GNB4, CCNA1 NPTX1 and C90RF19. Particularly the at least one gene can be selected from the group consisting of TFPI2, ARMC7, TRM_HUMAN, OGDHL, PTGS2, GPR39, C13ORF18, ASMTL, CCNA1, NPTX1 and DLL4. 
         [0088]    Kits according to the present invention are assemblages of reagents for testing methylation. They are typically in a package which contains all elements, optionally including instructions. The package may be divided so that components are not mixed until desired. Components may be in different physical states. For example, some components may be lyophilized and some in aqueous solution. Some may be frozen. Individual components may be separately packaged within the kit. The kit may contain reagents, as described above for differentially modifying methylated and non-methylated cytosine residues. Desirably the kit will contain oligonucleotide primers which specifically hybridize to regions within 1 kb of the transcription start sites of the genes/markers identified in the attached Table 5. Typically the kit will contain both a forward and a reverse primer for a single gene or marker. If there is a sufficient region of complementarity, e.g., 12, 15, 18, or 20 nucleotides, then the primer may also contain additional nucleotide residues that do not interfere with hybridization but may be useful for other manipulations. Exemplary of such other residues may be sites for restriction endonuclease cleavage, for ligand binding or for factor binding or linkers or repeats. The oligonucleotide primers may or may not be such that they are specific for modified methylated residues. The kit may optionally contain oligonucleotide probes. The probes may be specific for sequences containing modified methylated residues or for sequences containing non-methylated residues. The kit may optionally contain reagents for modifying methylated cytosine residues. The kit may also contain components for performing amplification, such as a DNA polymerase and deoxyribonucleotides. Means of detection may also be provided in the kit, including detectable labels on primers or probes. Kits may also contain reagents for detecting gene expression for one of the markers of the present invention (Table 5). Such reagents may include probes, primers, or antibodies, for example. In the case of enzymes or ligands, substrates or binding partners may be sued to assess the presence of the marker. 
         [0089]    In one aspect of this embodiment, the gene is contacted with hydrazine, which modifies cytosine residues, but not methylated cytosine residues, then the hydrazine treated gene sequence is contacted with a reagent such as piperidine, which cleaves the nucleic acid molecule at hydrazine modified cytosine residues, thereby generating a product comprising fragments. By separating the fragments according to molecular weight, using, for example, an electrophoretic, chromatographic, or mass spectrographic method, and comparing the separation pattern with that of a similarly treated corresponding non-methylated gene sequence, gaps are apparent at positions in the test gene contained methylated cytosine residues. As such, the presence of gaps is indicative of methylation of a cytosine residue in the CpG dinucleotide in the target gene of the test cell. 
         [0090]    Bisulfite ions, for example, sodium bisulfite, convert non-methylated cytosine residues to bisulfite modified cytosine residues. The bisulfite ion treated gene sequence can be exposed to alkaline conditions, which convert bisulfite modified cytosine residues to uracil residues. Sodium bisulfite reacts readily with the 5,6-double bond of cytosine (but poorly with methylated cytosine) to form a sulfonated cytosine reaction intermediate that is susceptible to deamination, giving rise to a sulfonated uracil. The sulfonate group can be removed by exposure to alkaline conditions, resulting in the formation of uracil. The DNA can be amplified, for example, by PCR, and sequenced to determine whether CpG sites are methylated in the DNA of the sample. Uracil is recognized as a thymine by Taq polymerase and, upon PCR, the resultant product contains cytosine only at the position where 5-methylcytosine was present in the starting template DNA. One can compare the amount or distribution of uracil residues in the bisulfite ion treated gene sequence of the test cell with a similarly treated corresponding non-methylated gene sequence. A decrease in the amount or distribution of uracil residues in the gene from the test cell indicates methylation of cytosine residues in CpG dinucleotides in the gene of the test cell. The amount or distribution of uracil residues also can be detected by contacting the bisulfite ion treated target gene sequence, following exposure to alkaline conditions, with an oligonucleotide that selectively hybridizes to a nucleotide sequence of the target gene that either contains uracil residues or that lacks uracil residues, but not both, and detecting selective hybridization (or the absence thereof) of the oligonucleotide. 
         [0091]    Any marker can be used for testing lung, prostate, breast or colon cells selected from the group consisting of CD3D, APOC1, NBL1, ING4, LEF1, CENTD3, MGC15396, FKBP4, PLTP, TFAP2A, ATXN1, BMP2, ENPEP, MCAM, SSBP2, PDLIM3, NDP, PHKA2, CBR3, CAMK4, HOXB5, ZNF198, RGS4, RBM15B, PDLIM3, PAK3, PIGH, TUBB4, NISCH, BACH1, CKMT, GALE, HMG20B, KRT14, OGDHL, PON2, SESN1, KIF1A (kinesin family member 1A) PDLIM3, MAL (T cell proliferation protein) B4GALT1, C10orf119, C10orf13, CBR1, COPS4, COVA1, CSRP1, DARS, DNAJC10, FKBP14, FN3KRP, GANAB, HUS1, KLF11, MRPL4, MYLK, NELF, NETO2, PAPSS2, RBMS2, RHOB, SECTM1, SIRT2, SIRT7, SLC35D1, SLC9A3R1, TTRAP, TUBG2, FLJ20277, MYBL2, GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. Markers which are useful for prostate cancer are CD3D, APOC1, NBL1, ING4, LEF1, CENTD3, MGC15396, FKBP4, PLTP, TFAP2A, ATXN1, BMP2, ENPEP, MCAM, SSBP2, PDLIM3, and NDP. Particularly useful among these are BMP2, ENPEP, MCAM, SSBP2, and NDP. Markers which are useful for lung cancer are PHKA2, CBR3, CAMK4, HOXB5, ZNF198, RGS4, RBM15B, PDLIM3, PAK3, PIGH, TUBB4, and NISCH. Particularly useful among these are PAK3, PIGH, TUBB4, and NISCH. Markers which are useful for breast cancer are BACH1, CKMT, GALE, HMG20B, KRT14, OGDHL, PON2, SESN1, KIF1A (kinesin family member 1A) PDLIM3 and MAL (T cell proliferation protein). Particularly useful among these are KIF1A (kinesin family member 1A) and MAL (T cell proliferation protein). Markers which are useful for colon cancer are B4GALT1, C10orf119, C10orf13, CBR1, COPS4, COVA1, CSRP1, DARS, DNAJC10, FKBP14, FN3KRP, GANAB, HUS1, KLF11, MRPL4, MYLK, NELF, NETO2, PAPSS2, RBMS2, RHOB, SECTM1, SIRT2, SIRT7, SLC35D1, SLC9A3R1, TTRAP, TUBG2, FLJ20277, MYBL2, GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. Particularly useful among these are GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. If the cell is a cervical cancer cell, at least one gene can be selected from the group consisting of PDCD4, TFPI2, ARMC7, TRM-HUMAN, OGDHL, PTGS2, CDK6, GPR39, HMGN2, C130RF18, ASMTL, DLL4, NP-659450.1, NP-078820.1, CLU, HPCA, PLCG2, RALY, GNB4, CCNA1 NPTX1 and C90RF19. Particularly the at least one gene can be selected from the group consisting of TFPI2, ARMC7, TRM_HUMAN, OGDHL, PTGS2, GPR39, C130RF18, ASMTL, CCNA1, NPTX1 and DLL4. 
         [0092]    Test compounds can be tested for their potential to treat cancer. Cancer cells for testing can be selected from the group consisting of prostate, lung, breast, and colon cancer. Expression of a gene selected from those listed in Table 5 is determined and if it is increased by the compound in the cell or if methylation of the gene is decreased by the compound in the cell, one can identify it as having potential as a treatment for cancer. For this purpose, the gene can be selected from the group consisting of CD3D, APOC1, NBL1, ING4, LEF1, CENTD3, MGC15396, FKBP4, PLTP, TFAP2A, ATXN1, BMP2, ENPEP, MCAM, SSBP2, PDLIM3, NDP, PHKA2, CBR3, CAMK4, HOXB5, ZNF198, RGS4, RBM15B, PDLIM3, PAK3, PIGH, TUBB4, NISCH, BACH1, CKMT, GALE, HMG20B, KRT14, OGDHL, PON2, SESN1, KIF1A (kinesin family member 1A) PDLIM3, MAL (T cell proliferation protein) B4GALT1, C10orf119, C10orf13, CBR1, COPS4, COVA1, CSRP1, DARS, DNAJC10, FKBP14, FN3KRP, GANAB, HUS1, KLF11, MRPL4, MYLK, NELF, NETO2, PAPSS2, RBMS2, RHOB, SECTM1, SIRT2, SIRT7, SLC35D1, SLC9A3R1, TTRAP, TUBG2, FLJ20277, MYBL2, GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. More particularly, the gene can be selected from the group consisting of BMP2, ENPEP, MCAM, SSBP2, NDP., PAK3, PIGH, TUBB4, and NISCH. KIF1A (kinesin family member 1A), MAL (T cell proliferation protein), GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. If the cell is a prostate cell, the gene can be selected from the group consisting of BMP2, ENPEP, MCAM, SSBP2, and NDP. If the cell is a lung cell, the gene can be selected from the group consisting of PAK3, PIGH, TUBB4, and NISCH. If the cell is a breast cell, the gene can be selected from the group consisting of KIF1A (kinesin family member 1A) and MAL (T cell proliferation protein). If the cell is a colon cell, the gene can be selected from the group consisting of GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. If the cell is a cervical cancer cell, at least one gene can be selected from the group consisting of PDCD4, TFPI2, ARMC7, TRM-HUMAN, OGDHL, PTGS2, CDK6, GPR39, HMGN2, C130RF18, ASMTL, DLL4, NP-659450.1, NP-078820.1, CLU, HPCA, PLCG2, RALY, GNB4, CCNA1 NPTX1 and C90RF19. Particularly the at least one gene can be selected from the group consisting of TFPI2, ARMC7, TRM_HUMAN, OGDHL, PTGS2, GPR39, C13ORF18, ASMTL, CCNA1, NPTX1 and DLL4. 
         [0093]    Alternatively such tests can be used to determine a prostate, lung, breast, or colon cancer patient&#39;s response to a chemotherapeutic agent. The patient can be treated with a chemotherapeutic agent. If expression of a gene selected from those listed in Table 5 is increased by the compound in cancer cells or if methylation of the gene is decreased by the compound in cancer cells it can be selected as useful for treatment of the patient. If the patient has cancer cells which are prostate, a lung, a breast, or colon, the gene can be selected from the group consisting of CD3D, APOC1, NBL1, ING4, LEF1, CENTD3, MGC15396, FKBP4, PLTP, TFAP2A, ATXN1, BMP2, ENPEP, MCAM, SSBP2, PDLIM3, NDP, PHKA2, CBR3, CAMK4, HOXB5, ZNF198, RGS4, RBM15B, PDLIM3, PAK3, PIGH, TUBB4, NISCH, BACH1, CKMT, GALE, HMG20B, KRT14, OGDHL, PON2, SESN1, KIF1A (kinesin family member 1A) PDLIM3, MAL (T cell proliferation protein) B4GALT1, C10orf119, C10orf13, CBR1, COPS4, COVA1, CSRP1, DARS, DNAJC10, FKBP14, FN3KRP, GANAB, HUS1, KLF11, MRPL4, MYLK, NELF, NETO2, PAPSS2, RBMS2, RHOB, SECTM1, SIRT2, SIRT7, SLC35D1, SLC9A3R1, TTRAP, TUBG2, FLJ20277, MYBL2, GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. More particularly, the marker or gene can be selected from the group consisting of BMP2, ENPEP, MCAM, SSBP2, NDP., PAK3, PIGH, TUBB4, and NISCH. KIF1A (kinesin family member 1A), MAL (T cell proliferation protein), GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. If the patient has prostate cancer, the gene can be selected from the group consisting of 3 MP2, ENPEP, MCAM, SSBP2, and NDP. If the patient has lung cancer, the gene can be selected from the group consisting of PAK3, PIGH, TUBB4, and NISCH. If the patient has breast cancer, the gene can be selected from the group consisting of KIF1A (kinesin family member 1A) and MAL (T cell proliferation protein). If the patient has colon cancer, the gene can be selected from the group consisting of GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21. If the cell is a cervical cancer cell, at least one gene can be selected from the group consisting of PDCD4, TFPI2, ARMC7, TRM-HUMAN, OGDHL, PTGS2, CDK6, GPR39, HMGN2, C130RF18, ASMTL, DLL4, NP-659450.1, NP-078820.1, CLU, HPCA, PLCG2, RALY, GNB4, CCNA1 NPTX1 and C90RF19. Particularly the at least one gene can be selected from the group consisting of TFPI2, ARMC7, TRM_HUMAN, OGDHL, PTGS2, GPR39, C13ORF18, ASMTL, CCNA1, NPTX1 and DLL4. 
         [0094]    According to additional aspects of the invention the finding of methylation of genes encoding proteins which are known to affect drug efficacy permits the use of methylation assays to predict response and stratify patients. For example, CBR-1 enhances the potency of doxorubicin, a chemotherapy drug. Methylation of the CBR-1 gene decreases the expression of CBR-1 thereby decreasing the potency of doxorubicin in the patient. Thus methylation of CBR-1 genes can be tested, and if found to be greater than in controls, than treatment with doxorubicin will be contraindicated. If methylation is not greater than in controls, such therapy is predicted to be efficacious. Similarly, methylation of genes such as TK-1, MYCK, and KCNJ8 can be used to predict drug efficacy and risk of disease. Methylation of TK-1 predicts a better response to DNA damaging agents, since TK-1 helps a cell circumvent the effects of DNA damaging agents. MYCK methylation can be used to predict the efficacy of methotrexate and mercaptopurinol treatment for leukemia. Similarly methylation of KCNJ8 can be used to predict risk of heart arrhythmia. 
         [0095]    The above disclosure generally describes the present invention. All references disclosed herein are expressly incorporated by reference. A more complete understanding can be obtained by reference to the following specific examples which are provided herein for purposes of illustration only, and are not intended to limit the scope of the invention. 
       Example 1 
     Methylation for Prostate Cancer 
       [0096]    Data were collected during a re-expression experiment using the prostate cancer cell lines 22rv1, DU145, LNACAP, and PC3. Expression levels of cells treated with 5 μM 5-Azacytidine (DAC) were compared to identical cell lines not treated with this reagent by hybridization to an Affymetrix HGU133A chip using a standard protocol. 
         [0097]    Analysis Strategy: 
         [0098]    A. The datasets containing information on around 23.000 genes were copied from the data archive on the ‘Methalyzer’ to a newly created directory. 
         [0099]    B. The needed details on the Affymetrix HGU133A chip were downloaded to the data analysis area of ‘Methalyzer’ 
         [0100]    C. The needed analysis tools (specific ‘R’ libraries for the bioconductor package) updated 
         [0101]    D. To estimate the raw data quality, two graphical overviews were created:
       Intensity plots for each chip on its own   RNA degradation plot       
 
         [0104]    E. Data sets were normalized together using the tool called ‘expresso’ applying the following parameters:
       Background correction: Mas   Normalization: quantiles   PM correction: Mas   Expression: Mas       
 
         [0109]    F. The result of the normalization was tested using a boxplot which displayed the intensity level calculated for each gene present on the chip. 
         [0110]    G. ‘P’ (present) ‘M’, (marginal) and ‘A’ (absent) calls made available by the MAS5 algorithm (Affymetrix software) for each gene and each experiment were collected and transferred to an Excel sheet. 
         [0111]    H. Using MS Excel, ‘P’ and ‘A’ calls were converted into an ‘Expression Score’ using the following rules:
       a. ‘P’ in the DAC treatment data sets got a score of 1   b. ‘A’ in the non-treatment data sets got a score of 1       
 
         [0114]    I. For each gene, the Expression Score was calculated 
         [0115]    J. A cut-off of 5 was defined as the first minimal criterion a gene had to fulfill 
         [0116]    K. As certain genes are present more than once on the chips used, a Perl script was created which allowed linking the probe set name on the chip and the corresponding RefSeq ID. 
         [0117]    L. The list of genes was restructured in such a way that each probe set was described in one row 
         [0118]    M. The table was transferred into a purpose built MS Access database 
         [0119]    N. A table containing the Methascores 2.2 of all described genes was added to the database system 
         [0120]    O. The following filtering rules were applied to the dataset
       a. X-chromosomal genes were excluded   b. Expression of the genes was ranked descending   c. Methascore 2.2 had to be &gt;3 and the number of different patterns per gene had to be &gt;3       
 
       Reactivated Genes are Shown in Table 4. 
     Example 2 
     Methylation for Lung Cancer 
       [0124]    Data were collected during re-expression experiments using squamous lung cancer cell lines HTB-58 and HTB-59 as well as lung adenocarcinoma cell lines A549 and H23. Expression levels in cells treated with 2 μM 5-Azacytidine (DAC) were compared to identical cell lines not treated with this reagent (PBS as replacement) by hybridization to Affymetrix HGU133A chip and the HGU95av2 chip using a standard protocol. 
         [0125]    Analysis Strategy: 
         [0126]    A. The datasets containing information on the probe sets were copied from the data archive on the ‘Methalyzer’ to a newly created directory. 
         [0127]    B. The needed details on the Affymetrix HGU133A chip and the HGU95av2 chip were downloaded to the data analysis area of ‘Methalyzer’ 
         [0128]    C. The needed analysis tools (specific ‘R’ libraries for the bioconductor package) updated 
         [0129]    D. To estimate the raw data quality, two graphical overviews were created:
       a. Boxplot of intensities for each chip before normalization   b. RNA degradation plot of each data set       
 
         [0132]    E. Data sets were normalized together using the tool called ‘expresso’ applying the following parameters:
       a. Background correction: Mas   b. Normalization: quantiles   c. PM correction: Mas   d. Expression: Mas       
 
         [0137]    F. The result of the normalization was tested using a boxplot which displayed the intensity level calculated for each gene present on the chip. 
         [0138]    G. ‘P’ (present) ‘M’, (marginal) and ‘A’ (absent) calls made available by the MAS5 algorithm (Affymetrix software) for each gene and each experiment were collected and transferred to an Excel sheet. 
         [0139]    H. Using MS Excel, ‘P’ and ‘A’ calls were converted into an ‘Expression Score’ using the following rules: 
         [0140]    a. ‘P’ in the DAC treatment data sets got a score of 1 
         [0141]    b. ‘A’ in the non-treatment data sets got a score of 1 
         [0142]    I. For each gene, the Expression Score was calculated 
         [0143]    J. A cut-off of 4 in the cans of squamous lung cancer cell lines and of 2 in the case of adenocarcinoma of the lung cell lines was defined as the first minimal criterion a gene had to fulfill 
         [0144]    K. As certain genes are present more than once on the chips used, a Perl script was created which allowed to link the probe set name on the chip and the corresponding RefSeq ID. 
         [0145]    L. The list of genes was restructured in such a way that each probe set was described in one row 
         [0146]    M. The table was transferred into a purpose built MS Access database 
         [0147]    N. A table containing the Methascores 2.2 of all described genes was added to the database system 
         [0148]    O. The following filtering rules were applied to the dataset 
         [0149]    a. X-chromosomal genes were excluded 
         [0150]    b. Expression scores were ranked descending and a cut-off of &gt;4 (squamous) and &gt;2 (adenocarcinoma of the lung) was set 
         [0151]    c. Methascore 2.2 cut-off was set to &gt;4 for both type of cell lines 
         [0152]    Reactivated genes are shown in Tables 1, 2, and 3 for squamous lung cancers, adenocarcinoma lung cancers, and both lung cancers. 
         [0153]    Summary analysis of both types of lung cancer cell lines: 
         [0154]    This study consisted of a comparison of the results achieved with both types of cell lines. As two different chip generations with different technical specifications and only few common probe sets were used, the results were compared on a list by list basis. Both data sets have been normalized within chips and across chips in the right concept. Given this, it can be assumed that the results are valid on their own. 
         [0155]    A comparison of the initial two lists indicated that there is one common element called “PLSC domain containing protein (LOC254531)”. This means that this marker can be used to detect both types of lung cancer but not to distinguish between both types of cancer. One additional marker for adenocarcinoma of the lung was found which doesn&#39;t occur in the squamous lung cancer cell line study (MCAM). 
       Example 3 
     Methylation for Colorectal Cancer 
       [0156]    Data were collected during a re-expression experiment using the colorectal cancer cell lines DLD-1, HCT116 and HT29. Expression of cells treated with 5 μM 5-Azacytidine (DAC) were compared to identical cell lines not treated with this reagent using a standard protocol and hybridization to Affymetrix HGU133A chips. 
         [0157]    Analysis Strategy: 
         [0158]    A. The datasets containing information on around 23.000 genes were copied from the data archive on the ‘Methalyzer’ to a newly created directory. 
         [0159]    B. The needed details on the Affymetrix HGU133A chip were downloaded to the data analysis area of ‘Methalyzer’ 
         [0160]    C. The needed analysis tools (specific ‘R’ libraries for the bioconductor package) updated 
         [0161]    D. To estimate the raw data quality, two graphical overviews were created:
       a. Intensity plots for each chip on its own   b. RNA degradation plot       
 
         [0164]    E. Data sets were normalized together using the tool called ‘expresso’ applying the following parameters:
       a. Background correction: Mas   b. Normalization: quantiles   c. PM correction: Mas   d. Expression: Mas       
 
         [0169]    F. The result of the normalization was tested using a boxplot which displayed the intensity level calculated for each gene present on the chip. 
         [0170]    G. ‘P’ (present) ‘M’, (marginal) and ‘A’ (absent) calls made available by the MAS5 algorithm (Affymetrix software) for each gene and each experiment were collected and transferred to an Excel sheet. 
         [0171]    H. Using MS Excel, ‘P’ and ‘A’ calls were converted into an ‘Expression Score’ using the following rules:
       a. ‘P’ in the DAC treatment data sets got a score of 1   b. ‘A’ in the non-treatment data sets got a score of 1       
 
         [0174]    I. For each gene, the Expression Score was calculated 
         [0175]    J. A cut-off of 4 was defined as the first minimal criterion a gene had to fulfill 
         [0176]    K. As certain genes are present more than once on the chips used, a Perl script was created which allowed to link the probe set name on the chip and the corresponding RefSeq ID. 
         [0177]    L. The list of genes was restructured in such a way that each probe set was described in one row 
         [0178]    M. The table was transferred into a purpose built MS Access database 
         [0179]    N. A table containing the Methascores  2 . 2  of all described genes was added to the database system 
         [0180]    O. The following filtering rules were applied to the dataset
       a. X-chromosomal genes were excluded   b. Expression of the genes was ranked descending   c. Methascore 2.2 had to be &gt;3 and the number of different patterns per gene had to be &gt;3       
 
         [0184]    Reactivated genes are shown in Table 7. 
       Example 4 
     Methylation for Cervix Cancer 
       [0185]    Data were collected during re-expression experiments of the four cell lines Hela, Siha, CSCC7 and CSCC8. The cell lines were treated with three different concentrations of 5-Azacytidine (DAC; 0.2 μM, 1 μM, 5 μM) using otherwise identical experimental conditions. 
         [0186]    Analysis Strategy: 
         [0000]    A. The datasets containing information on around 54.000 genes were copied from the data archive on the ‘Methalyzer’ to a newly created directory.
 
B. The needed details on the Affymetrix HGU133Aplus2.0 chip were downloaded to the data analysis area of ‘Methalyzer’
 
C. The needed analysis tools (specific ‘R’ libraries for the bioconductor package) updated
 
D. To estimate the raw data quality, two graphical overviews were created:
 
         [0187]    a. Intensity plots for each chip on its own 
         [0188]    b. RNA degradation plot 
         [0000]    E. Data sets were normalized together using the tool called ‘expresso’ applying the following parameters: 
         [0189]    a. Background correction: Mas 
         [0190]    b. Normalization: quantiles 
         [0191]    c. PM correction: Mas 
         [0192]    d. Expression: Mas 
         [0000]    F. The result of the normalization was tested using a boxplot which displayed the intensity level calculated for each gene present on the chip.
 
G. ‘P’ (present) ‘M’, (marginal) and ‘A’ (absent) calls made available by the MAS5 algorithm (Affymetrix software) for each gene and each experiment were collected and transferred to an Excel sheet.
 
H. Using MS Excel, ‘P’ and ‘A’ calls were converted into an ‘Expression Score’ using the following rules:
 
         [0193]    a. ‘P’ in the DAC treatment data sets got a score of 1 
         [0194]    b. ‘A’ in the non-treatment data sets got a score of 1 
         [0000]    I. For each gene and condition, the Expression Score was calculated
 
J. Lists were sorted based on a minimal expression score which was identical to the number of chips available for each condition
 
K. The Methascore cut-off was set to &gt;3 in all data sets
 
L. Lists were created detailing the conditions used and the markers selected
 
M. A summary was created which contained a condensed representation of the findings including an overview on which markers occurred under which condition.
 
         [0195]    Reactivated genes are shown in Table 8. 
       Example 5 
     Methylation for Breast Cancer 
       [0196]    Data were collected during a re-expression experiment using the breast cancer cell lines BT-20, MCF-7, MDA-MB 231 and MDA-MB 436. Expression levels of cells treated with 5 μM 5-Azacytidine (DAC; in acetic acid; were compared to identical cell lines not treated with this reagent (PBS as replacement) using an Affymetrix HGU133A chip. 
         [0197]    Analysis Strategy: 
         [0000]    A. The datasets containing information on around 23.000 genes were copied from the data archive on the ‘Methalyzer’ to a newly created directory.
 
B. The needed details on the Affymetrix HGU133A chip were downloaded to the data analysis area of ‘Methalyzer’
 
C. The needed analysis tools (specific ‘R’ libraries for the bioconductor package) updated
 
D. To estimate the raw data quality, two graphical overviews were created:
 
         [0198]    a. Intensity plots for each chip on its own 
         [0199]    b. RNA degradation plot 
         [0000]    E. Data sets were normalized together using the tool called ‘expresso’ applying the following parameters: 
         [0200]    a. Background correction: Mas 
         [0201]    b. Normalization: quantiles 
         [0202]    c. PM correction: Mas 
         [0203]    d. Expression: Mas 
         [0000]    F. The result of the normalization was tested using a boxplot which displayed the intensity level calculated for each gene present on the chip.
 
G. ‘P’ (present) ‘M’, (marginal) and ‘A’ (absent) calls made available by the MAS5 algorithm (Affymetrix software) for each gene and each experiment were collected and transferred to an Excel sheet.
 
H. Using MS Excel, ‘P’ and ‘A’ calls were converted into an ‘Expression Score’ using the following rules:
 
         [0204]    a. ‘P’ in the DAC treatment data sets got a score of 1 
         [0205]    b. ‘A’ in the non-treatment data sets got a score of 1 
         [0000]    I. For each gene, the Expression Score was calculated
 
J. A cut-off of 4 was defined as the first minimal criterion a gene had to fulfill
 
K. As certain genes are present more than once on the chips used, a Perl script was created which allowed to link the probe set name on the chip and the corresponding RefSeq ID.
 
L. The list of genes was restructured in such a way that each probe set was described in one row
 
M. The table was transferred into a purpose built MS Access database
 
N. A table containing the Methascores 2.2 of all described genes was added to the database system
 
O. The following filtering rules were applied to the dataset
 
         [0206]    a. X-chromosomal genes were excluded 
         [0207]    b. Expression scores were ranked descending and a cut-off of &gt;4 was set 
         [0208]    c. Methascore 2.2 cut-off was set to &gt;3 
         [0209]    Reactivated genes identified for breast are shown in Table 6. 
       Example 6 
     Cervical Cancer 
       [0210]    Three markers (CCNA1, NPTX1 and CACNA1C) were analyzed with Methylation Specific PCR in patient samples: 
         [0211]    CCNA1 and NPTX1 discriminate between cancers and normal cervixes (see  FIG. 1 ). 
         [0212]    CACNA1C→inadequate marker (methylated in cancers as well as in normal cervixes) 
         [0213]    For the other markers direct bisulfite sequencing (BSP) was performed on DNA derived from cervix samples from subjects without (normals) and with cervical cancer. Until now one (1) of the 24 tested markers showed methylation in the DNA from normals, 12 were unmethylated, 3 were almost completely unmethylated with the exception of one CG site and 8 were mostly unmethylated but showed methylation in more than 1 CG site. 
         [0214]    For 12 markers BSP results are available in cancer tissues: 10 of these contain methylated cytosines. The markers TFPI2, ARMC7, TRM_HUMAN, OGDHL, PTGS2, GPR39, C130RF18, ASMTL and DLL4 show differential methylation between the normals and the cancers cases. 
       Example 7 
     Prostate Cancer 
       [0215]    The methylation status of 47 genes was considered in the prostate cancer cell lines 22rv1; DU145; LNACAP and PC3. Markers CDH1, PTGS2, TWIST1, EDNRB, RUNX3, RARB, FANCF, FHIT and NMU have been reported previously to be methylated in prostate tissue or other tissue types. GLDC, RPS28, PODXL, ARIH2, ANAPC2, ARMC8, CSTF2T, POLA, FLJ10983, ZNF398, CBLL1, HSPB6, NF1, CEBPD, ARL4A, ARTS-1, ETFDH, PGEA1, HPN and WDR45 were found to be unmethylated in prostate cell lines. 
         [0216]    Sixteen out of 47 genes were shown to be methylated in at least some of the prostate cell lines by way of direct bisulfite sequencing. Genes NDP, CD3D, APOC1, NBL1, 
         [0217]    MCAM, ING4, LEF1, CENTD3, MGC15396 were methylated in all four cancer cell lines. FKBP4 was methylated in cell lines 22rv1, LNCaP and PC3; PLTP was methylated in cell lines 22rv1, LNCaP and PC3; genes ATXN1 and TFAP2A were methylated in cell lines DU145 and LNCaP; ENPEP was methylated in cell lines DU145 and PC3; SSBP2 was methylated in cell lines LNCaP and PC3 and gene BMP2 was methylated in cell line DU145. For other markers the methylation status was tested by way of MSP.  FIG. 2A  visualizes the result obtained for the CEBPC and PODXL genes in the different cell lines by way of MSP. 
         [0218]    The methylation status of the 16 genes was further tested in primary human prostate tissue and compared to their methylation status in normal prostate tissue from a non-prostate cancer patient. The markers BMP2, ENPEP, MCAM, SSBP2 and NDP show differential methylation between the normal prostate tissues and prostate cancer tissue or/and benign prostate hyperplasia. 
       Example 8 
     Lung Cancer 
       [0219]    The methylation status of 30 genes was considered in 15 lung adenoma-carcinoma/cancer cell lines by way of direct bisulfite sequencing or MSP. The Methprimer primer program was used to position the CpG island on the input sequence and to design primers. 
         [0220]    A total of 18 out of the 30 genes appeared to be unmethylated at the first CPG island (BS1) in the cell lines tested, whereas twelve out of 30 genes were methylated at BS1 in at least some of the lung cell lines. No CpG islands could be identified in the FMO4 gene 
         [0221]    Genes found to be unmethylated at BS1 were tested for their methylation status at subsequent CpG islands. One further gene, NISCH which was unmethylated at BS1 was found to be methylated at a further CpG island. 
         [0222]    The genes evidenced to be methylated in the tested cell lines, were further tested on methylation in 12 tumors and compared to 6 non-lung cancer patients. Table 18 indicates that markers PAK3, PIGH, TUBB4 and NISCH show differential methylation between the normals and the cancer cases. 
       Example 9 
     Breast Cancer 
       [0223]    Direct bisulfite sequencing or MSP was performed on DNA derived from different breast cancer cell lines (M12, BT20, M7, 231, 436 and HS578T). Genes BACH1, CKMT, GALE, HMG20B, KRT14, OGDHL, PON2, SESN1, KIF1A (kinesin family member 1A) and MAL (T cell proliferation protein) were methylated. 
         [0224]    Among the listed genes in table 19, those indicated by gray were found to be unmethylated in the tested cell lines, or they were methylated breast cancer cell lines as well as in primary paired normals. Genes indicated by blancs are left to finish sequencing in paired normal and tumor tissues. 
         [0225]    Genes which are non-methylated in normals, but which are methylated in breast cancer tissue can be used for identifying or prognosis of breast cancer. In particular methylation markers for breast cancer are KIF1A (kinesin family member 1A), MAL (T cell proliferation protein). 
       Example 10 
     Colon Cancer 
       [0226]    Direct bisulfite sequencing or MSP was performed on DNA derived from colon cancer cell lines. 
         [0227]    Bisulfite-sequencing. Bisulfite-modified genomic DNA was amplified by PCR using 10× buffer (166 mM (NH 4 ) 2 SO 4 , 670 mM Tris Buffer (pH 8.8), 67 mM MgCl 2 , 0.7% 2-mercaptoethanol, 1% DMSO), cervix, and primer sets that were designed to recognize DNA alterations after bisulfite treatment. Primer sequences are shown in Table in the PPT file; PCR reaction was performed for 45 cycles of 96° C. for 1 min, 54° C. for 1 min, and 72° C. for 1 min. PCR products were gel-extracted (Qiagen, Valencia, Calif.) and sequenced using the ABI BigDye cycle sequencing kit (Applied Biosystems, Foster City, Calif.). 
         [0228]    Conventional methylation-specific PCR (C-MSP). Bisulfite-treated DNA was amplified with either methylation-specific or unmethylation-specific primer sets by PCR using 10× buffer (166 mM (NH 4 ) 2 SO 4 , 670 mM Tris Buffer (pH 8.8), 67 mM MgCl 2 , 0.7% 2-mercaptoethanol, 1% DMSO) supplemented with 1.5 μl of 50 mM MgSO 4  for RGL-1, 1 μl of 50 mM MgSO 4  for B4GAL1 and BAG-1. PCR reaction was performed for 35 cycles of 95° C. for 30 sec, 59° C. for 30 sec, and 72° C. for 30 sec in 25 μl of reaction volume. 
         [0229]    All of the 36 genes B4GALT1, C10orf119, C10orf13, CBR1, COPS4, COVA1, CSRP1, DARS, DNAJC10, FKBP14, FN3KRP, GANAB, HUS1, KLF11, MRPL4, MYLK, NELF, NETO2, PAPSS2, RBMS2, RHOB, SECTM1, SIRT2, SIRT7, SLC35D1, SLC9A3R1, TTRAP, TUBG2, FLJ20277, MYBL2, GPR116, QSMR, PC4, SLC39A4, UBE3A, PDLIM3 and UBE21 appeared to be methylated in the colon cancer cell lines. The methylation status of the DNAJC10 gene was not uniform 
         [0230]    23 out of 26 genes were successfully sequenced in primary colon cancer tissues (Table 20). Differential methylation markers for colon cancer are GPR116, QSMR, PC4, SLC39A4, UBE23 and UBE21. Among 36 genes, 13 genes are left to finish sequencing in paired normal and tumor tissues. 
       REFERENCES 
       [0231]    The disclosure of each reference cited is expressly incorporated herein.
   Reeves et al., U.S. Pat. No. 6,596,493   Sidransky, U.S. Pat. No. 6,025,127   Sidransky, U.S. Pat. No. 5,561,041   Nelson et al., U.S. Pat. No. 5,552,277   Herman, et al., U.S. Pat. No. 6,017,704   Baylin et al, U.S. Patent Application Publication No. 2003/0224040 A1   Belinsky et al., U.S. Patent Application Publication No. 2004/0038245 A1   Sidransky, U.S. Patent Application Publication No. 2003/0124600 A1   Sidransky, U.S. Patent Application Publication No. 2004/0081976 A1   Sukumar et al., U.S. Pat. No. 6,756,200 B2   Herman et al., U.S. Patent Application Publication No. 2002/0127572 A1   
 
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 1 
               
               
                   
               
               
                 Lung Squamous 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 NM_000292 
                 Lung Squamous 
               
               
                   
                 NM_001236 
                 Lung Squamous 
               
               
                   
                 NM_002022 
                 Lung Squamous 
               
               
                   
                 NM_002397 
                 Lung Squamous 
               
               
                   
                 NM_002855 
                 Lung Squamous 
               
               
                   
                 NM_002937 
                 Lung Squamous 
               
               
                   
                 NM_004569 
                 Lung Squamous 
               
               
                   
                 NM_004720 
                 Lung Squamous 
               
               
                   
                 NM_005613 
                 Lung Squamous 
               
               
                   
                 NM_007184 
                 Lung Squamous 
               
               
                   
                 NM_013286 
                 Lung Squamous 
               
               
                   
                 NM_014288 
                 Lung Squamous 
               
               
                   
                 NM_014333 
                 Lung Squamous 
               
               
                   
                 NM_014570 
                 Lung Squamous 
               
               
                   
                 NM_031858 
                 Lung Squamous 
               
               
                   
                 NM_003378 
                 Lung Squamous, Breast 
               
               
                   
                 NM_005627 
                 Lung Squamous, Breast 
               
               
                   
                 NM_003896 
                 Lung Squamous, Breast, Colon 
               
               
                   
                 NM_001744 
                 Lung Squamous, Cervix 
               
               
                   
                 NM_000725 
                 Lung Squamous, Colon 
               
               
                   
                 NM_002486 
                 Lung Squamous, Colon 
               
               
                   
                 NM_002899 
                 Lung Squamous, Colon 
               
               
                   
                 NM_004385 
                 Lung Squamous, Colon 
               
               
                   
                 NM_005552 
                 Lung Squamous, Colon 
               
               
                   
                 NM_153613 
                 Lung Adeno, Lung Squamos, Colon 
               
               
                   
                 NM_006087 
                 Lung Adeno, Lung Squamos 
               
               
                   
                 NM_001645 
                 Prostate, Lung Adeno, Lung Squamos 
               
               
                   
                 NM_000115 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_000474 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_004453 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_015373 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_002151 
                 Prostate, Lung Squamos, Breast 
               
               
                   
                 NM_004360 
                 Prostate, Lung Squamos, Breast 
               
               
                   
                 NM_007075 
                 Prostate, Lung Squamos, Breast, Colon 
               
               
                   
                 NM_000963 
                 Prostate, Lung Squamos, Breast, Colon, Cervix 
               
               
                   
                 NM_001200 
                 Prostate, Lung Squamos, Colon 
               
               
                   
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 2 
               
               
                   
               
               
                 Lung Adeno 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 NM_001759 
                 Lung Adeno 
               
               
                   
                 NM_002147 
                 Lung Adeno 
               
               
                   
                 NM_002578 
                 Lung Adeno 
               
               
                   
                 NM_003012 
                 Lung Adeno 
               
               
                   
                 NM_003453 
                 Lung Adeno 
               
               
                   
                 NM_004817 
                 Lung Adeno 
               
               
                   
                 NM_005606 
                 Lung Adeno 
               
               
                   
                 NM_014476 
                 Lung Adeno 
               
               
                   
                 NM_016216 
                 Lung Adeno 
               
               
                   
                 NM_019102 
                 Lung Adeno 
               
               
                   
                 NM_006142 
                 Lung Adeno, Colon 
               
               
                   
                 NM_006087 
                 Lung Adeno, Lung Squamos 
               
               
                   
                 NM_153613 
                 Lung Adeno, Lung Squamos, Colon 
               
               
                   
                 NM_004192 
                 Lung AdenoCervix 
               
               
                   
                 NM_016269 
                 Prostate, Lung Adeno 
               
               
                   
                 NM_000266 
                 Prostate, Lung Adeno, Breast 
               
               
                   
                 NM_016442 
                 Prostate, Lung Adeno, Breast, Colon 
               
               
                   
                 NM_006500 
                 Prostate, Lung Adeno, Colon, Cervix 
               
               
                   
                 NM_001645 
                 Prostate, Lung Adeno, Lung Squamos 
               
               
                   
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 3 
               
               
                   
               
               
                 Lung (all) 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 NM_001759 
                 Lung Adeno 
               
               
                   
                 NM_002147 
                 Lung Adeno 
               
               
                   
                 NM_002578 
                 Lung Adeno 
               
               
                   
                 NM_003012 
                 Lung Adeno 
               
               
                   
                 NM_003453 
                 Lung Adeno 
               
               
                   
                 NM_004817 
                 Lung Adeno 
               
               
                   
                 NM_005606 
                 Lung Adeno 
               
               
                   
                 NM_014476 
                 Lung Adeno 
               
               
                   
                 NM_016216 
                 Lung Adeno 
               
               
                   
                 NM_019102 
                 Lung Adeno 
               
               
                   
                 NM_006142 
                 Lung Adeno, Colon 
               
               
                   
                 NM_006087 
                 Lung Adeno, Lung Squamos 
               
               
                   
                 NM_153613 
                 Lung Adeno, Lung Squamos, Colon 
               
               
                   
                 NM_004192 
                 Lung AdenoCervix 
               
               
                   
                 NM_000292 
                 Lung Squamos 
               
               
                   
                 NM_001236 
                 Lung Squamos 
               
               
                   
                 NM_002022 
                 Lung Squamos 
               
               
                   
                 NM_002397 
                 Lung Squamos 
               
               
                   
                 NM_002855 
                 Lung Squamos 
               
               
                   
                 NM_002937 
                 Lung Squamos 
               
               
                   
                 NM_004569 
                 Lung Squamos 
               
               
                   
                 NM_004720 
                 Lung Squamos 
               
               
                   
                 NM_005613 
                 Lung Squamos 
               
               
                   
                 NM_007184 
                 Lung Squamos 
               
               
                   
                 NM_013286 
                 Lung Squamos 
               
               
                   
                 NM_014288 
                 Lung Squamos 
               
               
                   
                 NM_014333 
                 Lung Squamos 
               
               
                   
                 NM_014570 
                 Lung Squamos 
               
               
                   
                 NM_031858 
                 Lung Squamos 
               
               
                   
                 NM_003378 
                 Lung Squamos, Breast 
               
               
                   
                 NM_005627 
                 Lung Squamos, Breast 
               
               
                   
                 NM_003896 
                 Lung Squamos, Breast, Colon 
               
               
                   
                 NM_001744 
                 Lung Squamos, Cervix 
               
               
                   
                 NM_000725 
                 Lung Squamos, Colon 
               
               
                   
                 NM_002486 
                 Lung Squamos, Colon 
               
               
                   
                 NM_002899 
                 Lung Squamos, Colon 
               
               
                   
                 NM_004385 
                 Lung Squamos, Colon 
               
               
                   
                 NM_005552 
                 Lung Squamos, Colon 
               
               
                   
                 NM_016269 
                 Prostate, Lung Adeno 
               
               
                   
                 NM_000266 
                 Prostate, Lung Adeno, Breast 
               
               
                   
                 NM_016442 
                 Prostate, Lung Adeno, Breast, Colon 
               
               
                   
                 NM_006500 
                 Prostate, Lung Adeno, Colon, Cervix 
               
               
                   
                 NM_001645 
                 Prostate, Lung Adeno, Lung Squamos 
               
               
                   
                 NM_000115 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_000474 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_004453 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_015373 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_002151 
                 Prostate, Lung Squamos, Breast 
               
               
                   
                 NM_004360 
                 Prostate, Lung Squamos, Breast 
               
               
                   
                 NM_007075 
                 Prostate, Lung Squamos, Breast, Colon 
               
               
                   
                 NM_000963 
                 Prostate, Lung Squamos, Breast, Colon, Cervix 
               
               
                   
                 NM_001200 
                 Prostate, Lung Squamos, Colon 
               
               
                   
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 4 
               
               
                   
               
               
                 Prostate 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 NM_000170 
                 Prostate 
               
               
                   
                 NM_000732 
                 Prostate 
               
               
                   
                 NM_000965 
                 Prostate 
               
               
                   
                 NM_001031 
                 Prostate 
               
               
                   
                 NM_001977 
                 Prostate 
               
               
                   
                 NM_002012 
                 Prostate 
               
               
                   
                 NM_003220 
                 Prostate 
               
               
                   
                 NM_005380 
                 Prostate 
               
               
                   
                 NM_005397 
                 Prostate 
               
               
                   
                 NM_005639 
                 Prostate 
               
               
                   
                 NM_006227 
                 Prostate 
               
               
                   
                 NM_006321 
                 Prostate 
               
               
                   
                 NM_006681 
                 Prostate 
               
               
                   
                 NM_012446 
                 Prostate 
               
               
                   
                 NM_013366 
                 Prostate 
               
               
                   
                 NM_014154 
                 Prostate 
               
               
                   
                 NM_015235 
                 Prostate 
               
               
                   
                 NM_016162 
                 Prostate 
               
               
                   
                 NM_016937 
                 Prostate 
               
               
                   
                 NM_018291 
                 Prostate 
               
               
                   
                 NM_018660 
                 Prostate 
               
               
                   
                 NM_022481 
                 Prostate 
               
               
                   
                 NM_022725 
                 Prostate 
               
               
                   
                 NM_024814 
                 Prostate 
               
               
                   
                 NM_144617 
                 Prostate 
               
               
                   
                 NM_000267 
                 Prostate, Breast, Cervix 
               
               
                   
                 NM_000332 
                 Prostate, Breast, Colon 
               
               
                   
                 NM_002014 
                 Prostate, Breast, Colon 
               
               
                   
                 NM_004350 
                 Prostate, Colon 
               
               
                   
                 NM_005195 
                 Prostate, Colon 
               
               
                   
                 NM_005738 
                 Prostate, Colon 
               
               
                   
                 NM_052855 
                 Prostate, Colon 
               
               
                   
                 NM_016269 
                 Prostate, Lung Adeno 
               
               
                   
                 NM_000266 
                 Prostate, Lung Adeno, Breast 
               
               
                   
                 NM_016442 
                 Prostate, Lung Adeno, Breast, Colon 
               
               
                   
                 NM_006500 
                 Prostate, Lung Adeno, Colon, Cervix 
               
               
                   
                 NM_001645 
                 Prostate, Lung Adeno, Lung Squamos 
               
               
                   
                 NM_000115 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_000474 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_004453 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_015373 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_002151 
                 Prostate, Lung Squamos, Breast 
               
               
                   
                 NM_004360 
                 Prostate, Lung Squamos, Breast 
               
               
                   
                 NM_007075 
                 Prostate, Lung Squamos, Breast, Colon 
               
               
                   
                 NM_000963 
                 Prostate, Lung Squamos, Breast, Colon, Cervix 
               
               
                   
                 NM_001200 
                 Prostate, Lung Squamos, Colon 
               
               
                   
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 5 
               
               
                   
               
               
                 All 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 NM_000122 
                 Breast 
               
               
                   
                 NM_000245 
                 Breast 
               
               
                   
                 NM_000305 
                 Breast 
               
               
                   
                 NM_000382 
                 Breast 
               
               
                   
                 NM_000403 
                 Breast 
               
               
                   
                 NM_000526 
                 Breast 
               
               
                   
                 NM_001037 
                 Breast 
               
               
                   
                 NM_001186 
                 Breast 
               
               
                   
                 NM_002371 
                 Breast 
               
               
                   
                 NM_004321 
                 Breast 
               
               
                   
                 NM_006013 
                 Breast 
               
               
                   
                 NM_007152 
                 Breast 
               
               
                   
                 NM_014242 
                 Breast 
               
               
                   
                 NM_014454 
                 Breast 
               
               
                   
                 NM_014630 
                 Breast 
               
               
                   
                 NM_014864 
                 Breast 
               
               
                   
                 NM_015277 
                 Breast 
               
               
                   
                 NM_015904 
                 Breast 
               
               
                   
                 NM_017895 
                 Breast 
               
               
                   
                 NM_017945 
                 Breast 
               
               
                   
                 NM_018067 
                 Breast 
               
               
                   
                 NM_020347 
                 Breast 
               
               
                   
                 NM_020990 
                 Breast 
               
               
                   
                 NM_138340 
                 Breast 
               
               
                   
                 NM_018245 
                 Breast, Cervix 
               
               
                   
                 NM_000038 
                 Breast, Colon 
               
               
                   
                 NM_003128 
                 Breast, Colon 
               
               
                   
                 NM_003359 
                 Breast, Colon 
               
               
                   
                 NM_006339 
                 Breast, Colon 
               
               
                   
                 NM_006815 
                 Breast, Colon 
               
               
                   
                 NM_012250 
                 Breast, Colon 
               
               
                   
                 NM_012316 
                 Breast, Colon 
               
               
                   
                 NM_015555 
                 Breast, Colon 
               
               
                   
                 NM_000719 
                 Cervix 
               
               
                   
                 NM_001259 
                 Cervix 
               
               
                   
                 NM_001508 
                 Cervix 
               
               
                   
                 NM_001831 
                 Cervix 
               
               
                   
                 NM_002143 
                 Cervix 
               
               
                   
                 NM_002522 
                 Cervix 
               
               
                   
                 NM_002618 
                 Cervix 
               
               
                   
                 NM_002661 
                 Cervix 
               
               
                   
                 NM_003400 
                 Cervix 
               
               
                   
                 NM_003787 
                 Cervix 
               
               
                   
                 NM_003914 
                 Cervix 
               
               
                   
                 NM_005517 
                 Cervix 
               
               
                   
                 NM_006528 
                 Cervix 
               
               
                   
                 NM_007367 
                 Cervix 
               
               
                   
                 NM_013312 
                 Cervix 
               
               
                   
                 NM_016084 
                 Cervix 
               
               
                   
                 NM_016368 
                 Cervix 
               
               
                   
                 NM_017722 
                 Cervix 
               
               
                   
                 NM_018380 
                 Cervix 
               
               
                   
                 NM_018389 
                 Cervix 
               
               
                   
                 NM_019062 
                 Cervix 
               
               
                   
                 NM_019074 
                 Cervix 
               
               
                   
                 NM_021629 
                 Cervix 
               
               
                   
                 NM_022064 
                 Cervix 
               
               
                   
                 NM_022131 
                 Cervix 
               
               
                   
                 NM_022147 
                 Cervix 
               
               
                   
                 NM_022343 
                 Cervix 
               
               
                   
                 NM_024034 
                 Cervix 
               
               
                   
                 NM_024072 
                 Cervix 
               
               
                   
                 NM_024537 
                 Cervix 
               
               
                   
                 NM_024544 
                 Cervix 
               
               
                   
                 NM_024585 
                 Cervix 
               
               
                   
                 NM_025113 
                 Cervix 
               
               
                   
                 NM_025158 
                 Cervix 
               
               
                   
                 NM_032756 
                 Cervix 
               
               
                   
                 NM_080669 
                 Cervix 
               
               
                   
                 NM_145013 
                 Cervix 
               
               
                   
                 NM_145341 
                 Cervix 
               
               
                   
                 NM_147193 
                 Cervix 
               
               
                   
                 NM_152643 
                 Cervix 
               
               
                   
                 NM_153355 
                 Cervix 
               
               
                   
                 NM_000182 
                 Colon 
               
               
                   
                 NM_001349 
                 Colon 
               
               
                   
                 NM_001677 
                 Colon 
               
               
                   
                 NM_001757 
                 Colon 
               
               
                   
                 NM_002412 
                 Colon 
               
               
                   
                 NM_002466 
                 Colon 
               
               
                   
                 NM_002658 
                 Colon 
               
               
                   
                 NM_002898 
                 Colon 
               
               
                   
                 NM_003004 
                 Colon 
               
               
                   
                 NM_003014 
                 Colon 
               
               
                   
                 NM_003345 
                 Colon 
               
               
                   
                 NM_003597 
                 Colon 
               
               
                   
                 NM_003876 
                 Colon 
               
               
                   
                 NM_003999 
                 Colon 
               
               
                   
                 NM_004040 
                 Colon 
               
               
                   
                 NM_004078 
                 Colon 
               
               
                   
                 NM_004252 
                 Colon 
               
               
                   
                 NM_004323 
                 Colon 
               
               
                   
                 NM_004507 
                 Colon 
               
               
                   
                 NM_004670 
                 Colon 
               
               
                   
                 NM_004935 
                 Colon 
               
               
                   
                 NM_005505 
                 Colon 
               
               
                   
                 NM_006180 
                 Colon 
               
               
                   
                 NM_006375 
                 Colon 
               
               
                   
                 NM_006703 
                 Colon 
               
               
                   
                 NM_006713 
                 Colon 
               
               
                   
                 NM_012237 
                 Colon 
               
               
                   
                 NM_014610 
                 Colon 
               
               
                   
                 NM_015049 
                 Colon 
               
               
                   
                 NM_015139 
                 Colon 
               
               
                   
                 NM_015149 
                 Colon 
               
               
                   
                 NM_015234 
                 Colon 
               
               
                   
                 NM_015537 
                 Colon 
               
               
                   
                 NM_015578 
                 Colon 
               
               
                   
                 NM_016129 
                 Colon 
               
               
                   
                 NM_016201 
                 Colon 
               
               
                   
                 NM_016437 
                 Colon 
               
               
                   
                 NM_016538 
                 Colon 
               
               
                   
                 NM_016614 
                 Colon 
               
               
                   
                 NM_017739 
                 Colon 
               
               
                   
                 NM_017767 
                 Colon 
               
               
                   
                 NM_017946 
                 Colon 
               
               
                   
                 NM_018092 
                 Colon 
               
               
                   
                 NM_018846 
                 Colon 
               
               
                   
                 NM_018981 
                 Colon 
               
               
                   
                 NM_024619 
                 Colon 
               
               
                   
                 NM_024834 
                 Colon 
               
               
                   
                 NM_030593 
                 Colon 
               
               
                   
                 NM_053030 
                 Colon 
               
               
                   
                 NM_130839 
                 Colon 
               
               
                   
                 NM_146388 
                 Colon 
               
               
                   
                 NM_001497 
                 Colon, Cervix 
               
               
                   
                 NM_001759 
                 Lung Adeno 
               
               
                   
                 NM_002147 
                 Lung Adeno 
               
               
                   
                 NM_002578 
                 Lung Adeno 
               
               
                   
                 NM_003012 
                 Lung Adeno 
               
               
                   
                 NM_003453 
                 Lung Adeno 
               
               
                   
                 NM_004817 
                 Lung Adeno 
               
               
                   
                 NM_005606 
                 Lung Adeno 
               
               
                   
                 NM_014476 
                 Lung Adeno 
               
               
                   
                 NM_016216 
                 Lung Adeno 
               
               
                   
                 NM_019102 
                 Lung Adeno 
               
               
                   
                 NM_006142 
                 Lung Adeno, Colon 
               
               
                   
                 NM_006087 
                 Lung Adeno, Lung Squamos 
               
               
                   
                 NM_153613 
                 Lung Adeno, Lung Squamos, Colon 
               
               
                   
                 NM_004192 
                 Lung Adeno Cervix 
               
               
                   
                 NM_000292 
                 Lung Squamos 
               
               
                   
                 NM_001236 
                 Lung Squamos 
               
               
                   
                 NM_002022 
                 Lung Squamos 
               
               
                   
                 NM_002397 
                 Lung Squamos 
               
               
                   
                 NM_002855 
                 Lung Squamos 
               
               
                   
                 NM_002937 
                 Lung Squamos 
               
               
                   
                 NM_004569 
                 Lung Squamos 
               
               
                   
                 NM_004720 
                 Lung Squamos 
               
               
                   
                 NM_005613 
                 Lung Squamos 
               
               
                   
                 NM_007184 
                 Lung Squamos 
               
               
                   
                 NM_013286 
                 Lung Squamos 
               
               
                   
                 NM_014288 
                 Lung Squamos 
               
               
                   
                 NM_014333 
                 Lung Squamos 
               
               
                   
                 NM_014570 
                 Lung Squamos 
               
               
                   
                 NM_031858 
                 Lung Squamos 
               
               
                   
                 NM_003378 
                 Lung Squamos, Breast 
               
               
                   
                 NM_005627 
                 Lung Squamos, Breast 
               
               
                   
                 NM_003896 
                 Lung Squamos, Breast, Colon 
               
               
                   
                 NM_001744 
                 Lung Squamos, Cervix 
               
               
                   
                 NM_000725 
                 Lung Squamos, Colon 
               
               
                   
                 NM_002486 
                 Lung Squamos, Colon 
               
               
                   
                 NM_002899 
                 Lung Squamos, Colon 
               
               
                   
                 NM_004385 
                 Lung Squamos, Colon 
               
               
                   
                 NM_005552 
                 Lung Squamos, Colon 
               
               
                   
                 NM_000170 
                 Prostate 
               
               
                   
                 NM_000732 
                 Prostate 
               
               
                   
                 NM_000965 
                 Prostate 
               
               
                   
                 NM_001031 
                 Prostate 
               
               
                   
                 NM_001977 
                 Prostate 
               
               
                   
                 NM_002012 
                 Prostate 
               
               
                   
                 NM_003220 
                 Prostate 
               
               
                   
                 NM_005380 
                 Prostate 
               
               
                   
                 NM_005397 
                 Prostate 
               
               
                   
                 NM_005639 
                 Prostate 
               
               
                   
                 NM_006227 
                 Prostate 
               
               
                   
                 NM_006321 
                 Prostate 
               
               
                   
                 NM_006681 
                 Prostate 
               
               
                   
                 NM_012446 
                 Prostate 
               
               
                   
                 NM_013366 
                 Prostate 
               
               
                   
                 NM_014154 
                 Prostate 
               
               
                   
                 NM_015235 
                 Prostate 
               
               
                   
                 NM_016162 
                 Prostate 
               
               
                   
                 NM_016937 
                 Prostate 
               
               
                   
                 NM_018291 
                 Prostate 
               
               
                   
                 NM_018660 
                 Prostate 
               
               
                   
                 NM_022481 
                 Prostate 
               
               
                   
                 NM_022725 
                 Prostate 
               
               
                   
                 NM_024814 
                 Prostate 
               
               
                   
                 NM_144617 
                 Prostate 
               
               
                   
                 NM_000267 
                 Prostate, Breast, Cervix 
               
               
                   
                 NM_000332 
                 Prostate, Breast, Colon 
               
               
                   
                 NM_002014 
                 Prostate, Breast, Colon 
               
               
                   
                 NM_004350 
                 Prostate, Colon 
               
               
                   
                 NM_005195 
                 Prostate, Colon 
               
               
                   
                 NM_005738 
                 Prostate, Colon 
               
               
                   
                 NM_052855 
                 Prostate, Colon 
               
               
                   
                 NM_016269 
                 Prostate, Lung Adeno 
               
               
                   
                 NM_000266 
                 Prostate, Lung Adeno, Breast 
               
               
                   
                 NM_016442 
                 Prostate, Lung Adeno, Breast, Colon 
               
               
                   
                 NM_006500 
                 Prostate, Lung Adeno, Colon, Cervix 
               
               
                   
                 NM_001645 
                 Prostate, Lung Adeno, Lung Squamos 
               
               
                   
                 NM_000115 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_000474 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_004453 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_015373 
                 Prostate, Lung Squamos 
               
               
                   
                 NM_002151 
                 Prostate, Lung Squamos, Breast 
               
               
                   
                 NM_004360 
                 Prostate, Lung Squamos, Breast 
               
               
                   
                 NM_007075 
                 Prostate, Lung Squamos, Breast, Colon 
               
               
                   
                 000963 
                 Prostate, Lung Squamos, Breast, Colon, Cervix 
               
               
                   
                 001200 
                 Prostate, Lung Squamos, Colon 
               
               
                   
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 6 
               
               
                   
               
               
                 Breast 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 NM_000122 
                 Breast 
               
               
                   
                 NM_000245 
                 Breast 
               
               
                   
                 NM_000305 
                 Breast 
               
               
                   
                 NM_000382 
                 Breast 
               
               
                   
                 NM_000403 
                 Breast 
               
               
                   
                 NM_000526 
                 Breast 
               
               
                   
                 NM_001037 
                 Breast 
               
               
                   
                 NM_001186 
                 Breast 
               
               
                   
                 NM_002371 
                 Breast 
               
               
                   
                 NM_004321 
                 Breast 
               
               
                   
                 NM_006013 
                 Breast 
               
               
                   
                 NM_007152 
                 Breast 
               
               
                   
                 NM_014242 
                 Breast 
               
               
                   
                 NM_014454 
                 Breast 
               
               
                   
                 NM_014630 
                 Breast 
               
               
                   
                 NM_014864 
                 Breast 
               
               
                   
                 NM_015277 
                 Breast 
               
               
                   
                 NM_015904 
                 Breast 
               
               
                   
                 NM_017895 
                 Breast 
               
               
                   
                 NM_017945 
                 Breast 
               
               
                   
                 NM_018067 
                 Breast 
               
               
                   
                 NM_020347 
                 Breast 
               
               
                   
                 NM_020990 
                 Breast 
               
               
                   
                 NM_138340 
                 Breast 
               
               
                   
                 NM_018245 
                 Breast, Cervix 
               
               
                   
                 NM_000038 
                 Breast, Colon 
               
               
                   
                 NM_003128 
                 Breast, Colon 
               
               
                   
                 NM_003359 
                 Breast, Colon 
               
               
                   
                 NM_006339 
                 Breast, Colon 
               
               
                   
                 NM_006815 
                 Breast, Colon 
               
               
                   
                 NM_012250 
                 Breast, Colon 
               
               
                   
                 NM_012316 
                 Breast, Colon 
               
               
                   
                 NM_015555 
                 Breast, Colon 
               
               
                   
                 NM_003378 
                 Lung Squamous, Breast 
               
               
                   
                 NM_005627 
                 Lung Squamous, Breast 
               
               
                   
                 NM_003896 
                 Lung Squamous, Breast, Colon 
               
               
                   
                 NM_000267 
                 Prostate, Breast, Cervix 
               
               
                   
                 NM_000332 
                 Prostate, Breast, Colon 
               
               
                   
                 NM_002014 
                 Prostate, Breast, Colon 
               
               
                   
                 NM_000266 
                 Prostate, Lung Adeno, Breast 
               
               
                   
                 NM_016442 
                 Prostate, Lung Adeno, Breast, Colon 
               
               
                   
                 NM_002151 
                 Prostate, Lung Squamos, Breast 
               
               
                   
                 NM_004360 
                 Prostate, Lung Squamos, Breast 
               
               
                   
                 NM_007075 
                 Prostate, Lung Squamos, Breast, Colon 
               
               
                   
                 NM_000963 
                 Prostate, Lung Squamos, Breast, Colon, Cervix 
               
               
                   
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 7 
               
               
                   
               
               
                 Colon 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 NM_000182 
                 Colon 
               
               
                   
                 NM_001349 
                 Colon 
               
               
                   
                 NM_001677 
                 Colon 
               
               
                   
                 NM_001757 
                 Colon 
               
               
                   
                 NM_002412 
                 Colon 
               
               
                   
                 NM_002466 
                 Colon 
               
               
                   
                 NM_002658 
                 Colon 
               
               
                   
                 NM_002898 
                 Colon 
               
               
                   
                 NM_003004 
                 Colon 
               
               
                   
                 NM_003014 
                 Colon 
               
               
                   
                 NM_003345 
                 Colon 
               
               
                   
                 NM_003597 
                 Colon 
               
               
                   
                 NM_003876 
                 Colon 
               
               
                   
                 NM_003999 
                 Colon 
               
               
                   
                 NM_004040 
                 Colon 
               
               
                   
                 NM_004078 
                 Colon 
               
               
                   
                 NM_004252 
                 Colon 
               
               
                   
                 NM_004323 
                 Colon 
               
               
                   
                 NM_004507 
                 Colon 
               
               
                   
                 NM_004670 
                 Colon 
               
               
                   
                 NM_004935 
                 Colon 
               
               
                   
                 NM_005505 
                 Colon 
               
               
                   
                 NM_006180 
                 Colon 
               
               
                   
                 NM_006375 
                 Colon 
               
               
                   
                 NM_006703 
                 Colon 
               
               
                   
                 NM_006713 
                 Colon 
               
               
                   
                 NM_012237 
                 Colon 
               
               
                   
                 NM_014610 
                 Colon 
               
               
                   
                 NM_015049 
                 Colon 
               
               
                   
                 NM_015139 
                 Colon 
               
               
                   
                 NM_015149 
                 Colon 
               
               
                   
                 NM_015234 
                 Colon 
               
               
                   
                 NM_015537 
                 Colon 
               
               
                   
                 NM_015578 
                 Colon 
               
               
                   
                 NM_016129 
                 Colon 
               
               
                   
                 NM_016201 
                 Colon 
               
               
                   
                 NM_016437 
                 Colon 
               
               
                   
                 NM_016538 
                 Colon 
               
               
                   
                 NM_016614 
                 Colon 
               
               
                   
                 NM_017739 
                 Colon 
               
               
                   
                 NM_017767 
                 Colon 
               
               
                   
                 NM_017946 
                 Colon 
               
               
                   
                 NM_018092 
                 Colon 
               
               
                   
                 NM_018846 
                 Colon 
               
               
                   
                 NM_018981 
                 Colon 
               
               
                   
                 NM_024619 
                 Colon 
               
               
                   
                 NM_024834 
                 Colon 
               
               
                   
                 NM_030593 
                 Colon 
               
               
                   
                 NM_053030 
                 Colon 
               
               
                   
                 NM_130839 
                 Colon 
               
               
                   
                 NM_146388 
                 Colon 
               
               
                   
                 NM_001497 
                 Colon, Cervix 
               
               
                   
                 NM_000725 
                 Lung Squamous, Colon 
               
               
                   
                 NM_002486 
                 Lung Squamous, Colon 
               
               
                   
                 NM_002899 
                 Lung Squamous, Colon 
               
               
                   
                 NM_004385 
                 Lung Squamous, Colon 
               
               
                   
                 NM_005552 
                 Lung Squamous, Colon 
               
               
                   
                 NM_003896 
                 Lung Squamous, Breast, Colon 
               
               
                   
                 NM_153613 
                 Lung Adeno, Lung Squamos, Colon 
               
               
                   
                 NM_006142 
                 Lung Adeno, Colon 
               
               
                   
                 NM_007075 
                 Prostate, Lung Squamos, Breast, Colon 
               
               
                   
                 NM_000963 
                 Prostate, Lung Squamos, Breast, Colon, Cervix 
               
               
                   
                 NM_001200 
                 Prostate, Lung Squamos, Colon 
               
               
                   
                 NM_016442 
                 Prostate, Lung Adeno, Breast, Colon 
               
               
                   
                 NM_000332 
                 Prostate, Breast, Colon 
               
               
                   
                 NM_002014 
                 Prostate, Breast, Colon 
               
               
                   
                 NM_004350 
                 Prostate, Colon 
               
               
                   
                 NM_005195 
                 Prostate, Colon 
               
               
                   
                 NM_005738 
                 Prostate, Colon 
               
               
                   
                 NM_052855 
                 Prostate, Colon 
               
               
                   
                 NM_000038 
                 Breast, Colon 
               
               
                   
                 NM_003128 
                 Breast, Colon 
               
               
                   
                 NM_003359 
                 Breast, Colon 
               
               
                   
                 NM_006339 
                 Breast, Colon 
               
               
                   
                 NM_006815 
                 Breast, Colon 
               
               
                   
                 NM_012250 
                 Breast, Colon 
               
               
                   
                 NM_012316 
                 Breast, Colon 
               
               
                   
                 NM_015555 
                 Breast, Colon 
               
               
                   
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 8 
               
               
                   
               
               
                 Cervix 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 NM_000719 
                 Cervix 
               
               
                   
                 NM_001259 
                 Cervix 
               
               
                   
                 NM_001508 
                 Cervix 
               
               
                   
                 NM_001831 
                 Cervix 
               
               
                   
                 NM_002143 
                 Cervix 
               
               
                   
                 NM_002522 
                 Cervix 
               
               
                   
                 NM_002618 
                 Cervix 
               
               
                   
                 NM_002661 
                 Cervix 
               
               
                   
                 NM_003400 
                 Cervix 
               
               
                   
                 NM_003787 
                 Cervix 
               
               
                   
                 NM_003914 
                 Cervix 
               
               
                   
                 NM_005517 
                 Cervix 
               
               
                   
                 NM_006528 
                 Cervix 
               
               
                   
                 NM_007367 
                 Cervix 
               
               
                   
                 NM_013312 
                 Cervix 
               
               
                   
                 NM_016084 
                 Cervix 
               
               
                   
                 NM_016368 
                 Cervix 
               
               
                   
                 NM_017722 
                 Cervix 
               
               
                   
                 NM_018380 
                 Cervix 
               
               
                   
                 NM_018389 
                 Cervix 
               
               
                   
                 NM_019062 
                 Cervix 
               
               
                   
                 NM_019074 
                 Cervix 
               
               
                   
                 NM_021629 
                 Cervix 
               
               
                   
                 NM_022064 
                 Cervix 
               
               
                   
                 NM_022131 
                 Cervix 
               
               
                   
                 NM_022147 
                 Cervix 
               
               
                   
                 NM_022343 
                 Cervix 
               
               
                   
                 NM_024034 
                 Cervix 
               
               
                   
                 NM_024072 
                 Cervix 
               
               
                   
                 NM_024537 
                 Cervix 
               
               
                   
                 NM_024544 
                 Cervix 
               
               
                   
                 NM_024585 
                 Cervix 
               
               
                   
                 NM_025113 
                 Cervix 
               
               
                   
                 NM_025158 
                 Cervix 
               
               
                   
                 NM_032756 
                 Cervix 
               
               
                   
                 NM_080669 
                 Cervix 
               
               
                   
                 NM_145013 
                 Cervix 
               
               
                   
                 NM_145341 
                 Cervix 
               
               
                   
                 NM_147193 
                 Cervix 
               
               
                   
                 NM_152643 
                 Cervix 
               
               
                   
                 NM_153355 
                 Cervix 
               
               
                   
                 NM_001744 
                 Lung Squamous, Cervix 
               
               
                   
                 NM_004192 
                 Lung AdenoCervix 
               
               
                   
                 NM_000267 
                 Prostate, Breast, Cervix 
               
               
                   
                 NM_006500 
                 Prostate, Lung Adeno, Colon, Cervix 
               
               
                   
                 NM_000963 
                 Prostate, Lung Squamos, Breast, Colon, Cervix 
               
               
                   
                 NM_018245 
                 Breast, Cervix 
               
               
                   
                 NM_001497 
                 Colon, Cervix 
               
               
                   
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 15 
               
               
                   
               
               
                 210.nm2np.txt 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 NM_000038 
                 NP_000029 
               
               
                   
                 NM_000115 
                 NP_000106 
               
               
                   
                 NM_000122 
                 NP_000113 
               
               
                   
                 NM_000170 
                 NP_000161 
               
               
                   
                 NM_000182 
                 NP_000173 
               
               
                   
                 NM_000245 
                 NP_000236 
               
               
                   
                 NM_000266 
                 NP_000257 
               
               
                   
                 NM_000267 
                 NP_000258 
               
               
                   
                 NM_000292 
                 NP_000283 
               
               
                   
                 NM_000305 
                 NP_000296 
               
               
                   
                 NM_000332 
                 NP_000323 
               
               
                   
                 NM_000382 
                 NP_000373 
               
               
                   
                 NM_000403 
                 NP_000394 
               
               
                   
                 NM_000474 
                 NP_000465 
               
               
                   
                 NM_000526 
                 NP_000517 
               
               
                   
                 NM_000719 
                 NP_000710 
               
               
                   
                 NM_000725 
                 NP_000716 
               
               
                   
                 NM_000732 
                 NP_000723 
               
               
                   
                 NM_000963 
                 NP_000954 
               
               
                   
                 NM_000965 
                 NP_000956 
               
               
                   
                 NM_001031 
                 NP_001022 
               
               
                   
                 NM_001037 
                 NP_001028 
               
               
                   
                 NM_001186 
                 NP_001177 
               
               
                   
                 NM_001200 
                 NP_001191 
               
               
                   
                 NM_001236 
                 NP_001227 
               
               
                   
                 NM_001259 
                 NP_001250 
               
               
                   
                 NM_001349 
                 NP_001340 
               
               
                   
                 NM_001497 
                 NP_001488 
               
               
                   
                 NM_001508 
                 NP_001499 
               
               
                   
                 NM_001645 
                 NP_001636 
               
               
                   
                 NM_001677 
                 NP_001668 
               
               
                   
                 NM_001744 
                 NP_001735 
               
               
                   
                 NM_001757 
                 NP_001748 
               
               
                   
                 NM_001759 
                 NP_001750 
               
               
                   
                 NM_001831 
                 NP_001822 
               
               
                   
                 NM_001977 
                 NP_001968 
               
               
                   
                 NM_002012 
                 NP_002003 
               
               
                   
                 NM_002014 
                 NP_002005 
               
               
                   
                 NM_002022 
                 NP_002013 
               
               
                   
                 NM_002143 
                 NP_002134 
               
               
                   
                 NM_002147 
                 NP_002138 
               
               
                   
                 NM_002151 
                 NP_002142 
               
               
                   
                 NM_002371 
                 NP_002362 
               
               
                   
                 NM_002397 
                 NP_002388 
               
               
                   
                 NM_002412 
                 NP_002403 
               
               
                   
                 NM_002466 
                 NP_002457 
               
               
                   
                 NM_002486 
                 NP_002477 
               
               
                   
                 NM_002522 
                 NP_002513 
               
               
                   
                 NM_002578 
                 NP_002569 
               
               
                   
                 NM_002618 
                 NP_002609 
               
               
                   
                 NM_002658 
                 NP_002649 
               
               
                   
                 NM_002661 
                 NP_002652 
               
               
                   
                 NM_002855 
                 NP_002846 
               
               
                   
                 NM_002898 
                 NP_002889 
               
               
                   
                 NM_002899 
                 NP_002890 
               
               
                   
                 NM_002937 
                 NP_002928 
               
               
                   
                 NM_003004 
                 NP_002995 
               
               
                   
                 NM_003012 
                 NP_003003 
               
               
                   
                 NM_003014 
                 NP_003005 
               
               
                   
                 NM_003128 
                 NP_003119 
               
               
                   
                 NM_003220 
                 NP_003211 
               
               
                   
                 NM_003345 
                 NP_003336 
               
               
                   
                 NM_003359 
                 NP_003350 
               
               
                   
                 NM_003378 
                 NP_003369 
               
               
                   
                 NM_003400 
                 NP_003391 
               
               
                   
                 NM_003453 
                 NP_003444 
               
               
                   
                 NM_003597 
                 NP_003588 
               
               
                   
                 NM_003787 
                 NP_003778 
               
               
                   
                 NM_003876 
                 NP_003867 
               
               
                   
                 NM_003896 
                 NP_003887 
               
               
                   
                 NM_003914 
                 NP_003905 
               
               
                   
                 NM_003999 
                 NP_003990 
               
               
                   
                 NM_004040 
                 NP_004031 
               
               
                   
                 NM_004078 
                 NP_004069 
               
               
                   
                 NM_004192 
                 NP_004183 
               
               
                   
                 NM_004252 
                 NP_004243 
               
               
                   
                 NM_004321 
                 NP_004312 
               
               
                   
                 NM_004323 
                 NP_004314 
               
               
                   
                 NM_004350 
                 NP_004341 
               
               
                   
                 NM_004360 
                 NP_004351 
               
               
                   
                 NM_004385 
                 NP_004376 
               
               
                   
                 NM_004453 
                 NP_004444 
               
               
                   
                 NM_004507 
                 NP_004498 
               
               
                   
                 NM_004569 
                 NP_004560 
               
               
                   
                 NM_004670 
                 NP_004661 
               
               
                   
                 NM_004720 
                 NP_004711 
               
               
                   
                 NM_004817 
                 NP_004808 
               
               
                   
                 NM_004935 
                 NP_004926 
               
               
                   
                 NM_005195 
                 NP_005186 
               
               
                   
                 NM_005380 
                 NP_005371 
               
               
                   
                 NM_005397 
                 NP_005388 
               
               
                   
                 NM_005505 
                 NP_005496 
               
               
                   
                 NM_005517 
                 NP_005508 
               
               
                   
                 NM_005552 
                 NP_005543 
               
               
                   
                 NM_005606 
                 NP_005597 
               
               
                   
                 NM_005613 
                 NP_005604 
               
               
                   
                 NM_005627 
                 NP_005618 
               
               
                   
                 NM_005639 
                 NP_005630 
               
               
                   
                 NM_005738 
                 NP_005729 
               
               
                   
                 NM_006013 
                 NP_006004 
               
               
                   
                 NM_006087 
                 NP_006078 
               
               
                   
                 NM_006142 
                 NP_006133 
               
               
                   
                 NM_006180 
                 NP_006171 
               
               
                   
                 NM_006227 
                 NP_006218 
               
               
                   
                 NM_006321 
                 NP_006312 
               
               
                   
                 NM_006339 
                 NP_006330 
               
               
                   
                 NM_006375 
                 NP_006366 
               
               
                   
                 NM_006500 
                 NP_006491 
               
               
                   
                 NM_006528 
                 NP_006519 
               
               
                   
                 NM_006681 
                 NP_006672 
               
               
                   
                 NM_006703 
                 NP_006694 
               
               
                   
                 NM_006713 
                 NP_006704 
               
               
                   
                 NM_006815 
                 NP_006806 
               
               
                   
                 NM_007075 
                 NP_009006 
               
               
                   
                 NM_007152 
                 NP_009083 
               
               
                   
                 NM_007184 
                 NP_009115 
               
               
                   
                 NM_007367 
                 NP_031393 
               
               
                   
                 NM_012237 
                 NP_036369 
               
               
                   
                 NM_012250 
                 NP_036382 
               
               
                   
                 NM_012316 
                 NP_036448 
               
               
                   
                 NM_012446 
                 NP_036578 
               
               
                   
                 NM_013286 
                 NP_037418 
               
               
                   
                 NM_013312 
                 NP_037444 
               
               
                   
                 NM_013366 
                 NP_037498 
               
               
                   
                 NM_014154 
                 NP_054873 
               
               
                   
                 NM_014242 
                 NP_055057 
               
               
                   
                 NM_014288 
                 NP_055103 
               
               
                   
                 NM_014333 
                 NP_055148 
               
               
                   
                 NM_014454 
                 NP_055269 
               
               
                   
                 NM_014476 
                 NP_055291 
               
               
                   
                 NM_014570 
                 NP_055385 
               
               
                   
                 NM_014610 
                 NP_055425 
               
               
                   
                 NM_014630 
                 NP_055445 
               
               
                   
                 NM_014864 
                 NP_055679 
               
               
                   
                 NM_015049 
                 NP_055864 
               
               
                   
                 NM_015139 
                 NP_055954 
               
               
                   
                 NM_015149 
                 NP_055964 
               
               
                   
                 NM_015234 
                 NP_056049 
               
               
                   
                 NM_015235 
                 NP_056050 
               
               
                   
                 NM_015277 
                 NP_056092 
               
               
                   
                 NM_015373 
                 NP_056188 
               
               
                   
                 NM_015537 
                 NP_056352 
               
               
                   
                 NM_015555 
                 NP_056370 
               
               
                   
                 NM_015578 
                 NP_056393 
               
               
                   
                 NM_015904 
                 NP_056988 
               
               
                   
                 NM_016084 
                 NP_057168 
               
               
                   
                 NM_016129 
                 NP_057213 
               
               
                   
                 NM_016162 
                 NP_057246 
               
               
                   
                 NM_016201 
                 NP_057285 
               
               
                   
                 NM_016216 
                 NP_057300 
               
               
                   
                 NM_016269 
                 NP_057353 
               
               
                   
                 NM_016368 
                 NP_057452 
               
               
                   
                 NM_016437 
                 NP_057521 
               
               
                   
                 NM_016442 
                 NP_057526 
               
               
                   
                 NM_016538 
                 NP_057622 
               
               
                   
                 NM_016614 
                 NP_057698 
               
               
                   
                 NM_016937 
                 NP_058633 
               
               
                   
                 NM_017722 
                 NP_060192 
               
               
                   
                 NM_017739 
                 NP_060209 
               
               
                   
                 NM_017767 
                 NP_060237 
               
               
                   
                 NM_017895 
                 NP_060365 
               
               
                   
                 NM_017945 
                 NP_060415 
               
               
                   
                 NM_017946 
                 NP_060416 
               
               
                   
                 NM_018067 
                 NP_060537 
               
               
                   
                 NM_018092 
                 NP_060562 
               
               
                   
                 NM_018245 
                 NP_060715 
               
               
                   
                 NM_018291 
                 NP_060761 
               
               
                   
                 NM_018380 
                 NP_060850 
               
               
                   
                 NM_018389 
                 NP_060859 
               
               
                   
                 NM_018660 
                 NP_061130 
               
               
                   
                 NM_018846 
                 NP_061334 
               
               
                   
                 NM_018981 
                 NP_061854 
               
               
                   
                 NM_019062 
                 NP_061935 
               
               
                   
                 NM_019074 
                 NP_061947 
               
               
                   
                 NM_019102 
                 NP_061975 
               
               
                   
                 NM_020347 
                 NP_065080 
               
               
                   
                 NM_020990 
                 NP_066270 
               
               
                   
                 NM_021629 
                 NP_067642 
               
               
                   
                 NM_022064 
                 NP_071347 
               
               
                   
                 NM_022131 
                 NP_071414 
               
               
                   
                 NM_022147 
                 NP_071430 
               
               
                   
                 NM_022343 
                 NP_071738 
               
               
                   
                 NM_022481 
                 NP_071926 
               
               
                   
                 NM_022725 
                 NP_073562 
               
               
                   
                 NM_024034 
                 NP_076939 
               
               
                   
                 NM_024072 
                 NP_076977 
               
               
                   
                 NM_024537 
                 NP_078813 
               
               
                   
                 NM_024544 
                 NP_078820 
               
               
                   
                 NM_024585 
                 NP_078861 
               
               
                   
                 NM_024619 
                 NP_078895 
               
               
                   
                 NM_024814 
                 NP_079090 
               
               
                   
                 NM_024834 
                 NP_079110 
               
               
                   
                 NM_025113 
                 NP_079389 
               
               
                   
                 NM_025158 
                 NP_079434 
               
               
                   
                 NM_030593 
                 NP_085096 
               
               
                   
                 NM_031858 
                 NP_114064 
               
               
                   
                 NM_032756 
                 NP_116145 
               
               
                   
                 NM_052855 
                 NP_443087 
               
               
                   
                 NM_053030 
                 NP_444258 
               
               
                   
                 NM_080669 
                 NP_542400 
               
               
                   
                 NM_130839 
                 NP_570854 
               
               
                   
                 NM_138340 
                 NP_612213 
               
               
                   
                 NM_144617 
                 NP_653218 
               
               
                   
                 NM_145013 
                 NP_659450 
               
               
                   
                 NM_145341 
                 NP_663314 
               
               
                   
                 NM_146388 
                 NP_666500 
               
               
                   
                 NM_147193 
                 NP_671726 
               
               
                   
                 NM_152643 
                 NP_689856 
               
               
                   
                 NM_153355 
                 NP_699186 
               
               
                   
                 NM_153613 
                 NP_705841 
               
               
                   
                   
               
               
                   
                 Tool completed successfully 
               
             
          
         
       
     
         [0000]    
       
         
               
               
               
               
               
             
           
               
                 TABLE 16 
               
               
                   
               
               
                   
                 BSP 
                   
                   
                   
               
               
                   
                 amplicon 
                 BSP sequencing 2 
                 BSP sequencing 10 
                 Differential results 
               
               
                 Gene 
                 length 
                 normals 
                 cancers 
                 normals versus cancers 
               
               
                   
               
             
             
               
                 PDCD4 
                 391 
                 M 
                   
                   
               
               
                 PEX13 
                 296 
                 Un 
                 Un 
               
               
                 TFPI2 
                 367 
                 Un 
                 M 
                 x 
               
               
                 ARMC7 
                 404 
                 Un 
                 M 
                 x 
               
               
                 TRM_HUMAN 
                 344 
                 Un 
                 M 
                 x 
               
               
                 OGDHL 
                 382 
                 Un 
                 M 
                 x 
               
               
                 RNF123 
                 402 
                 Un 
                 Un 
               
               
                 PTGS2 
                 406 
                 Un 
                 M 
                 x 
               
               
                 CDK6 
                 450 
                 Un 
               
               
                 CDK6 
                 385 
                 Un 
               
               
                 GPR39 
                 377 
                 Un 
                 M 
                 x 
               
               
                 HMGN2 
                 383 
                 Un 
               
               
                 C13ORF18 
                 248 
                 Un 
                 M 
                 x 
               
               
                 ASMTL 
                 328 
                 Un, 1 CG + 
                 M 
                 x 
               
               
                 DLL4 
                 461 
                 Un, 1 CG+ 
               
               
                 DLL4 
                 226 
                 Un, 1 CG+ 
                 M 
                 x 
               
               
                 NP_659450.1 
                 392 
                 Un, some CG+ 
                 M 
                 ? 
               
               
                 NP_078820.1 
                 444 
                 Un, some CG+ 
               
               
                 CLU 
                 445 
                 Un, some CG+ 
               
               
                 HPCA 
                 368 
                 Un, some CG+ 
               
               
                 PLCG2 
                 444 
                 Un, some CG+ 
               
               
                 RALY 
                 314 
                 Un, some CG+ 
               
               
                 GNB4 
                 340 
                 Un, some CG+ 
                 in middle M, rest Un 
               
               
                 C9ORF19 
                 443 
                 Un, some CG+ 
               
               
                   
               
               
                 Blank = missing data 
               
               
                 un = unmethylated 
               
               
                 M = methylated 
               
               
                 CG+ = methylation positive CG sequence 
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
             
           
               
                 TABLE 17 
               
               
                   
               
               
                 Accession number correlation to gene/protein name 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 NM_000038.3| Homo sapiens  adenomatosis polyposis coli (APC); 
               
               
                 NM_000115.1| Homo sapiens  endothelin receptor type B (EDNRB), transcript variant 1; 
               
               
                 NM_000122.1| Homo sapiens  excision repair cross-complementing rodent repair deficiency, 
               
               
                 complementation group 3 (xeroderma pigmentosum group B complementing) (ERCC3); 
               
               
                 NM_000170.1| Homo sapiens  glycine dehydrogenase (decarboxylating; glycine 
               
               
                 decarboxylase, glycine cleavage system protein P) (GLDC); 
               
               
                 NM_000182.3| Homo sapiens  hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl- 
               
               
                 Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit 
               
               
                 (HADHA); 
               
               
                 NM_000245.2| Homo sapiens  met proto-oncogene (hepatocyte growth factor receptor) 
               
               
                 (MET); 
               
               
                 NM_000266.1| Homo sapiens  Norrie disease (pseudoglioma) (NDP); 
               
               
                 NM_000267.1| Homo sapiens  neurofibromin 1 (neurofibromatosis, von Recklinghausen 
               
               
                 disease, Watson disease) (NF1); 
               
               
                 NM_000292.1| Homo sapiens  phosphorylase kinase, alpha 2 (liver) (PHKA2); 
               
               
                 NM_000305.1| Homo sapiens  paraoxonase 2 (PON2); 
               
               
                 NM_000332.2| Homo sapiens  ataxin 1 (ATXN1); 
               
               
                 NM_000382.1| Homo sapiens  aldehyde dehydrogenase 3 family, member A2 (ALDH3A2); 
               
               
                 NM_000403.3| Homo sapiens  UDP-galactose-4-epimerase (GALE), transcript variant 1; 
               
               
                 NM_000474.2| Homo sapiens  twist homolog 1 (acrocephalosyndactyly 3; Saethre-Chotzen 
               
               
                 syndrome) ( Drosophila ) (TWIST1); 
               
               
                 NM_000526.3| Homo sapiens  keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, 
               
               
                 Koebner) (KRT14); 
               
               
                 NM_000719.4| Homo sapiens  calcium channel, voltage-dependent, L type, alpha 1C subunit 
               
               
                 (CACNA1C); 
               
               
                 NM_000725.2| Homo sapiens  calcium channel, voltage-dependent, beta 3 subunit 
               
               
                 (CACNB3); 
               
               
                 NM_000732.3| Homo sapiens  CD3D antigen, delta polypeptide (TiT3 complex) (CD3D); 
               
               
                 NM_000963.1| Homo sapiens  prostaglandin-endoperoxide synthase 2 (prostaglandin G/H 
               
               
                 synthase and cyclooxygenase) (PTGS2); 
               
               
                 NM_000965.2| Homo sapiens  retinoic acid receptor, beta (RARB), transcript variant 1; 
               
               
                 NM_001031.2| Homo sapiens  ribosomal protein S28 (RPS28); 
               
               
                 NM_001037.3| Homo sapiens  sodium channel, voltage-gated, type I, beta (SCN1B), 
               
               
                 transcript variant a; 
               
               
                 NM_001186.2| Homo sapiens  BTB and CNC homology 1, basic leucine zipper transcription 
               
               
                 factor 1 (BACH1), transcript variant 2; 
               
               
                 NM_001200.1| Homo sapiens  bone morphogenetic protein 2 (BMP2); 
               
               
                 NM_001236.3| Homo sapiens  carbonyl reductase 3 (CBR3); 
               
               
                 NM_001259.5| Homo sapiens  cyclin-dependent kinase 6 (CDK6); 
               
               
                 NM_001349.2| Homo sapiens  aspartyl-tRNA synthetase (DARS); 
               
               
                 NM_001497.2| Homo sapiens  UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, 
               
               
                 polypeptide 1 (B4GALT1); 
               
               
                 NM_001508.1| Homo sapiens  G protein-coupled receptor 39 (GPR39); 
               
               
                 NM_001645.3| Homo sapiens  apolipoprotein C-I (APOC1); 
               
               
                 NM_001677.3| Homo sapiens  ATPase, Na+/K+ transporting, beta 1 polypeptide (ATP1B1), 
               
               
                 transcript variant 1; 
               
               
                 NM_001744.3| Homo sapiens  calcium/calmodulin-dependent protein kinase IV (CAMK4); 
               
               
                 NM_001757.2| Homo sapiens  carbonyl reductase 1 (CBR1); 
               
               
                 NM_001759.2| Homo sapiens  cyclin D2 (CCND2); 
               
               
                 NM_001831.2| Homo sapiens  clusterin (complement lysis inhibitor, SP-40,40, sulfated 
               
               
                 glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J) (CLU), transcript 
               
               
                 variant 1; 
               
               
                 NM_001977.2| Homo sapiens  glutamyl aminopeptidase (aminopeptidase A) (ENPEP); 
               
               
                 NM_002012.1| Homo sapiens  fragile histidine triad gene (FHIT); 
               
               
                 NM_002014.2| Homo sapiens  FK506 binding protein 4, 59 kDa (FKBP4); 
               
               
                 NM_002022.1| Homo sapiens  flavin containing monooxygenase 4 (FMO4); 
               
               
                 NM_002143.2| Homo sapiens  hippocalcin (HPCA); 
               
               
                 NM_002147.2| Homo sapiens  homeo box B5 (HOXB5); 
               
               
                 NM_002151.1| Homo sapiens  hepsin (transmembrane protease, serine 1) (HPN), transcript 
               
               
                 variant 2; 
               
               
                 NM_002371.2| Homo sapiens  mal, T-cell differentiation protein (MAL), transcript variant a; 
               
               
                 NM_002397.2| Homo sapiens  MADS box transcription enhancer factor 2, polypeptide C 
               
               
                 (myocyte enhancer factor 2C) (MEF2C); 
               
               
                 NM_002412.2| Homo sapiens  O-6-methylguanine-DNA methyltransferase (MGMT); 
               
               
                 NM_002466.2| Homo sapiens  v-myb myeloblastosis viral oncogene homolog (avian)-like 2 
               
               
                 (MYBL2); 
               
               
                 NM_002486.3| Homo sapiens  nuclear cap binding protein subunit 1, 80 kDa (NCBP1); 
               
               
                 NM_002522.2| Homo sapiens  neuronal pentraxin I (NPTX1); 
               
               
                 NM_002578.2| Homo sapiens  p21 (CDKN1A)-activated kinase 3 (PAK3); 
               
               
                 NM_002618.2| Homo sapiens  peroxisome biogenesis factor 13 (PEX13); 
               
               
                 NM_002658.2| Homo sapiens  plasminogen activator, urokinase (PLAU); 
               
               
                 NM_002661.1| Homo sapiens  phospholipase C, gamma 2 (phosphatidylinositol-specific) 
               
               
                 (PLCG2); 
               
               
                 NM_002855.3| Homo sapiens  poliovirus receptor-related 1 (herpesvirus entry mediator C; 
               
               
                 nectin) (PVRL1), transcript variant 1; 
               
               
                 NM_002898.2| Homo sapiens  RNA binding motif, single stranded interacting protein 2 
               
               
                 (RBMS2); 
               
               
                 NM_002899.2| Homo sapiens  retinol binding protein 1, cellular (RBP1); 
               
               
                 NM_002937.3| Homo sapiens  ribonuclease, RNase A family, 4 (RNASE4), transcript variant 
               
               
                 2; 
               
               
                 NM_003004.1| Homo sapiens  secreted and transmembrane 1 (SECTM1); 
               
               
                 M_003012.3| Homo sapiens  secreted frizzled-related protein 1 (SFRP1); 
               
               
                 NM_003014.2| Homo sapiens  secreted frizzled-related protein 4 (SFRP4); 
               
               
                 NM_003128.1| Homo sapiens  spectrin, beta, non-erythrocytic 1 (SPTBN1), transcript variant 
               
               
                 1; 
               
               
                 NM_003220.1| Homo sapiens  transcription factor AP-2 alpha (activating enhancer binding 
               
               
                 protein 2 alpha) (TFAP2A); 
               
               
                 NM_003345.3| Homo sapiens  ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast) 
               
               
                 (UBE2I), transcript variant 1; 
               
               
                 NM_003359.1| Homo sapiens  UDP-glucose dehydrogenase (UGDH); 
               
               
                 NM_003378.2| Homo sapiens  VGF nerve growth factor inducible (VGF); 
               
               
                 NM_003400.3| Homo sapiens  exportin 1 (CRM1 homolog, yeast) (XPO1); 
               
               
                 NM_003453.2| Homo sapiens  zinc finger protein 198 (ZNF198); 
               
               
                 NM_003597.4| Homo sapiens  Kruppel-like factor 11 (KLF11); 
               
               
                 NM_003787.1| Homo sapiens  nucleolar protein 4 (NOL4); 
               
               
                 NM_003876.1| Homo sapiens  chromosome 17 open reading frame 35 (C17orf35); 
               
               
                 NM_003896.2| Homo sapiens  ST3 beta-galactoside alpha-2,3-sialyltransferase 5 
               
               
                 (ST3GAL5); 
               
               
                 NM_003914.2| Homo sapiens  cyclin A1 (CCNA1); 
               
               
                 NM_003999.1| Homo sapiens  oncostatin M receptor (OSMR); 
               
               
                 NM_004040.2| Homo sapiens  ras homolog gene family, member B (RHOB); 
               
               
                 NM_004078.1| Homo sapiens  cysteine and glycine-rich protein 1 (CSRP1); 
               
               
                 NM_004192.1| Homo sapiens  acetylserotonin O-methyltransferase-like (ASMTL); 
               
               
                 NM_004252.1| Homo sapiens  solute carrier family 9 (sodium/hydrogen exchanger), isoform 
               
               
                 3 regulator 1 (SLC9A3R1); 
               
               
                 NM_004321.4| Homo sapiens  kinesin family member 1A (KIF1A); 
               
               
                 NM_004323.2| Homo sapiens  BCL2-associated athanogene (BAG1); 
               
               
                 NM_004350.1| Homo sapiens  runt-related transcription factor 3 (RUNX3); 
               
               
                 NM_004360.2| Homo sapiens  cadherin 1, type 1, E-cadherin (epithelial) (CDH1); 
               
               
                 NM_004385.2| Homo sapiens  chondroitin sulfate proteoglycan 2 (versican) (CSPG2); 
               
               
                 NM_004453.1| Homo sapiens  electron-transferring-flavoprotein dehydrogenase (ETFDH), 
               
               
                 nuclear gene encoding mitochondrial protein; 
               
               
                 NM_004507.2| Homo sapiens  HUS1 checkpoint homolog ( S. pombe ) (HUS1); 
               
               
                 NM_004569.2| Homo sapiens  phosphatidylinositol glycan, class H (PIGH); 
               
               
                 NM_004670.2| Homo sapiens  3′-phosphoadenosine 5′-phosphosulfate synthase 2 (PAPSS2); 
               
               
                 NM_004720.4| Homo sapiens  endothelial differentiation, lysophosphatidic acid G-protein- 
               
               
                 coupled receptor, 4 (EDG4); 
               
               
                 NM_004817.2| Homo sapiens  tight junction protein 2 (zona occludens 2) (TJP2), transcript 
               
               
                 variant 1; 
               
               
                 NM_004935.2| Homo sapiens  cyclin-dependent kinase 5 (CDK5); 
               
               
                 NM_005195.2| Homo sapiens  CCAAT/enhancer binding protein (C/EBP), delta (CEBPD); 
               
               
                 NM_005380.3| Homo sapiens  neuroblastoma, suppression of tumorigenicity 1 (NBL1), 
               
               
                 transcript variant 2; 
               
               
                 NM_005397.2| Homo sapiens  podocalyxin-like (PODXL); 
               
               
                 NM_005505.3| Homo sapiens  scavenger receptor class B, member 1 (SCARB1); 
               
               
                 NM_005517.2| Homo sapiens  high-mobility group nucleosomal binding domain 2 
               
               
                 (HMGN2); 
               
               
                 NM_005552.3| Homo sapiens  kinesin 2 60/70 kDa (KNS2); 
               
               
                 M_005606.5| Homo sapiens  legumain (LGMN), transcript variant 1; 
               
               
                 NM_005613.3| Homo sapiens  regulator of G-protein signalling 4 (RGS4); 
               
               
                 M_005627.2| Homo sapiens  serum/glucocorticoid regulated kinase (SGK); 
               
               
                 NM_005639.1| Homo sapiens  synaptotagmin I (SYT1); 
               
               
                 NM_005738.2| Homo sapiens  ADP-ribosylation factor-like 4A (ARL4A), transcript variant 
               
               
                 1; 
               
               
                 NM_006013.2| Homo sapiens  ribosomal protein L10 (RPL10); 
               
               
                 NM_006087.2| Homo sapiens  tubulin, beta 4 (TUBB4); 
               
               
                 NM_006142.3| Homo sapiens  stratifin (SFN); 
               
               
                 NM_006180.2| Homo sapiens  neurotrophic tyrosine kinase, receptor, type 2 (NTRK2); 
               
               
                 NM_006227.2| Homo sapiens  phospholipid transfer protein (PLTP), transcript variant 1; 
               
               
                 NM_006321.1| Homo sapiens  ariadne homolog 2 ( Drosophila ) (ARIH2); 
               
               
                 NM_006339.1| Homo sapiens  high-mobility group 20B (HMG20B); 
               
               
                 NM_006375.2| Homo sapiens  cytosolic ovarian carcinoma antigen 1 (COVA1), transcript 
               
               
                 variant 1; 
               
               
                 NM_006500.1| Homo sapiens  melanoma cell adhesion molecule (MCAM); 
               
               
                 NM_006528.2| Homo sapiens  tissue factor pathway inhibitor 2 (TFPI2); 
               
               
                 NM_006681.1| Homo sapiens  neuromedin U (NMU); 
               
               
                 NM_006703.2| Homo sapiens  nudix (nucleoside diphosphate linked moiety X)-type motif 3 
               
               
                 (NUDT3); 
               
               
                 NM_006713.2| Homo sapiens  activated RNA polymerase II transcription cofactor 4 (PC4); 
               
               
                 NM_006815.2| Homo sapiens  coated vesicle membrane protein (RNP24); 
               
               
                 NM_007075.2| Homo sapiens  WD repeat domain 45 (WDR45); 
               
               
                 NM_007152.1| Homo sapiens  zinc finger protein 195 (ZNF195); 
               
               
                 NM_007184.1| Homo sapiens  nischarin (NISCH); 
               
               
                 NM_007367.2| Homo sapiens  RNA binding protein (autoantigenic, hnRNP-associated with 
               
               
                 lethal yellow) (RALY), transcript variant 2; 
               
               
                 NM_012237.2| Homo sapiens  sirtuin (silent mating type information regulation 2 homolog) 2 
               
               
                 ( S. cerevisiae ) (SIRT2), transcript variant 1; 
               
               
                 NM_012250.3| Homo sapiens  related RAS viral (r-ras) oncogene homolog 2 (RRAS2); 
               
               
                 NM_012316.3| Homo sapiens  karyopherin alpha 6 (importin alpha 7) (KPNA6); 
               
               
                 M_012446.2| Homo sapiens  single-stranded DNA binding protein 2 (SSBP2); 
               
               
                 NM_013286.3| Homo sapiens  RNA binding motif protein 15B (RBM15B); 
               
               
                 NM_013312.1| Homo sapiens  hook homolog 2 ( Drosophila ) (HOOK2); 
               
               
                 NM_013366.3| Homo sapiens  anaphase promoting complex subunit 2 (ANAPC2); 
               
               
                 NM_014154.2| Homo sapiens  armadillo repeat containing 8 (ARMC8); 
               
               
                 NM_014242.1| Homo sapiens  zinc finger protein 237 (ZNF237); 
               
               
                 NM_014288.3| Homo sapiens  integrin beta 3 binding protein (beta3-endonexin) (ITGB3BP); 
               
               
                 NM_014333.2| Homo sapiens  immunoglobulin superfamily, member 4 (IGSF4); 
               
               
                 NM_014454.1| Homo sapiens  sestrin 1 (SESN1); 
               
               
                 NM_014476.1| Homo sapiens  PDZ and LIM domain 3 (PDLIM3); 
               
               
                 NM_014570.3| Homo sapiens  ADP-ribosylation factor GTPase activating protein 3 
               
               
                 (ARFGAP3); 
               
               
                 NM_014610.3| Homo sapiens  glucosidase, alpha; neutral AB (GANAB); 
               
               
                 NM_014630.1| Homo sapiens  zinc finger protein 592 (ZNF592); 
               
               
                 NM_014864.2| Homo sapiens  family with sequence similarity 20, member B (FAM20B); 
               
               
                 NM_015049.1| Homo sapiens  amyotrophic lateral sclerosis 2 (juvenile) chromosome region, 
               
               
                 candidate 3 (ALS2CR3); 
               
               
                 NM_015139.1| Homo sapiens  solute carrier family 35 (UDP-glucuronic acid/UDP-N- 
               
               
                 acetylgalactosamine dual transporter), member D1 (SLC35D1); 
               
               
                 NM_015149.2| Homo sapiens  ral guanine nucleotide dissociation stimulator-like 1 (RGL1); 
               
               
                 NM_015234.3| Homo sapiens  G protein-coupled receptor 116 (GPR116); 
               
               
                 NM_015235.2| Homo sapiens  cleavage stimulation factor, 3′ pre-RNA, subunit 2, 64 kDa, tau 
               
               
                 variant (CSTF2T); 
               
               
                 NM_015277.2| Homo sapiens  neural precursor cell expressed, developmentally down- 
               
               
                 regulated 4-like (NEDD4L); 
               
               
                 NM_015373.3| Homo sapiens  PKD2 interactor, golgi and endoplasmic reticulum associated 1 
               
               
                 (PGEA1), transcript variant 1; 
               
               
                 NM_015537.3| Homo sapiens  nasal embryonic LHRH factor (NELF); 
               
               
                 NM_015555.1| Homo sapiens  zinc finger protein 451 (ZNF451); 
               
               
                 NM_015578.1| Homo sapiens  family with sequence similarity 61, member A (FAM61A); 
               
               
                 NM_015904.2| Homo sapiens  eukaryotic translation initiation factor 5B (EIF5B); 
               
               
                 NM_016084.3| Homo sapiens  RAS, dexamethasone-induced 1 (RASD1); 
               
               
                 NM_016129.2| Homo sapiens  COP9 constitutive photomorphogenic homolog subunit 4 
               
               
                 ( Arabidopsis ) (COPS4); 
               
               
                 NM_016162.2| Homo sapiens  inhibitor of growth family, member 4 (ING4), transcript 
               
               
                 variant 1; 
               
               
                 NM_016201.2| Homo sapiens  angiomotin like 2 (AMOTL2); 
               
               
                 NM_016216.2| Homo sapiens  debranching enzyme homolog 1 ( S. cerevisiae ) (DBR1); 
               
               
                 NM_016269.2| Homo sapiens  lymphoid enhancer-binding factor 1 (LEF1); 
               
               
                 NM_016368.3| Homo sapiens  myo-inositol 1-phosphate synthase A1 (ISYNA1); 
               
               
                 NM_016437.1| Homo sapiens  tubulin, gamma 2 (TUBG2); 
               
               
                 NM_016442.2| Homo sapiens  type 1 tumor necrosis factor receptor shedding aminopeptidase 
               
               
                 regulator (ARTS-1); 
               
               
                 NM_016538.1| Homo sapiens  sirtuin (silent mating type information regulation 2 homolog) 7 
               
               
                 ( S. cerevisiae ) (SIRT7); 
               
               
                 NM_016614.2| Homo sapiens  TRAF and TNF receptor associated protein (TTRAP); 
               
               
                 NM_016937.1| Homo sapiens  polymerase (DNA directed), alpha (POLA); 
               
               
                 NM_017722.2| Homo sapiens  hypothetical protein FLJ20244 (FLJ20244); 
               
               
                 NM_017739.1| Homo sapiens  O-linked mannose beta1,2-N-acetylglucosaminyltransferase 
               
               
                 (POMGNT1); 
               
               
                 NM_017767.1| Homo sapiens  solute carrier family 39 (zinc transporter), member 4 
               
               
                 (SLC39A4); 
               
               
                 NM_017895.6| Homo sapiens  DEAD (Asp-Glu-Ala-Asp) box polypeptide 27 (DDX27); 
               
               
                 NM_017945.2| Homo sapiens  solute carrier family 35, member A5 (SLC35A5); 
               
               
                 NM_017946.2| Homo sapiens  FK506 binding protein 14, 22 kDa (FKBP14); 
               
               
                 NM_018067.2| Homo sapiens  hypothetical protein FLJ10350 (FLJ10350); 
               
               
                 NM_018092.3| Homo sapiens  neuropilin (NRP) and tolloid (TLL)-like 2 (NETO2); 
               
               
                 NM_018245.1| Homo sapiens  oxoglutarate dehydrogenase-like (OGDHL); 
               
               
                 NM_018291.2| Homo sapiens  hypothetical protein FLJ10986 (FLJ10986); 
               
               
                 NM_018380.2| Homo sapiens  DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 (DDX28), 
               
               
                 nuclear gene encoding mitochondrial protein; 
               
               
                 NM_018389.3| Homo sapiens  solute carrier family 35, member C1 (SLC35C1); 
               
               
                 NM_018660.2| Homo sapiens  zinc finger protein 395 (ZNF395); 
               
               
                 NM_018846.2| Homo sapiens  kelch-like 7 ( Drosophila ) (KLHL7); 
               
               
                 NM_018981.1| Homo sapiens  DnaJ (Hsp40) homolog, subfamily C, member 10 (DNAJC10); 
               
               
                 NM_019062.1| Homo sapiens  ring finger protein 186 (RNF186); 
               
               
                 NM_019074.2| Homo sapiens  delta-like 4 ( Drosophila ) (DLL4); 
               
               
                 NM_019102.2| Homo sapiens  homeo box A5 (HOXA5); 
               
               
                 NM_020347.2| Homo sapiens  leucine zipper transcription factor-like 1 (LZTFL1); 
               
               
                 NM_020990.2| Homo sapiens  creatine kinase, mitochondrial 1 (ubiquitous) (CKMT1), 
               
               
                 nuclear gene encoding mitochondrial protein; 
               
               
                 NM_021629.2| Homo sapiens  guanine nucleotide binding protein (G protein), beta 
               
               
                 polypeptide 4 (GNB4); 
               
               
                 NM_022064.2| Homo sapiens  ring finger protein 123 (RNF123); 
               
               
                 NM_022131.1| Homo sapiens  calsyntenin 2 (CLSTN2); 
               
               
                 NM_022147.2| Homo sapiens  28 kD interferon responsive protein (IFRG28); 
               
               
                 NM_022343.2| Homo sapiens  chromosome 9 open reading frame 19 (C9orf19); 
               
               
                 NM_022481.5| Homo sapiens  centaurin, delta 3 (CENTD3); 
               
               
                 NM_022725.2| Homo sapiens  Fanconi anemia, complementation group F (FANCF); 
               
               
                 NM_024034.3| Homo sapiens  ganglioside-induced differentiation-associated protein 1-like 1 
               
               
                 (GDAP1L1); 
               
               
                 NM_024072.3| Homo sapiens  DEAD (Asp-Glu-Ala-Asp) box polypeptide 54 (DDX54); 
               
               
                 NM_024537.1| Homo sapiens  hypothetical protein FLJ12118 (FLJ12118); 
               
               
                 NM_024544.1| Homo sapiens  hypothetical protein FLJ12875 (FLJ12875); 
               
               
                 NM_024585.2| Homo sapiens  armadillo repeat containing 7 (ARMC7); 
               
               
                 NM_024619.2| Homo sapiens  fructosamine-3-kinase-related protein (FN3KRP); 
               
               
                 NM_024814.1| Homo sapiens  Cas-Br-M (murine) ecotropic retroviral transforming 
               
               
                 sequence-like 1 (CBLL1); 
               
               
                 NM_024834.1| Homo sapiens  chromosome 10 open reading frame 119 (C10orf119); 
               
               
                 NM_025113.1| Homo sapiens  chromosome 13 open reading frame 18 (C13orf18); 
               
               
                 NM_025158.2| Homo sapiens  RUN and FYVE domain containing 1 (RUFY1); 
               
               
                 NM_030593.1| Homo sapiens  sirtuin (silent mating type information regulation 2 homolog) 2 
               
               
                 ( S. cerevisiae ) (SIRT2), transcript variant 2; 
               
               
                 NM_031858.1| Homo sapiens  neighbor of BRCA1 gene 1 (NBR1), transcript variant 2; 
               
               
                 NM_032756.2| Homo sapiens  hypothetical protein MGC15668 (MGC15668); 
               
               
                 NM_052855.2| Homo sapiens  hypothetical protein MGC15396 (MGC15396); 
               
               
                 NM_053030.2| Homo sapiens  myosin, light polypeptide kinase (MYLK), transcript variant 5; 
               
               
                 NM_080669.2| Homo sapiens  similar to RIKEN cDNA 1110002C08 gene (MGC9564); 
               
               
                 NM_130839.1| Homo sapiens  ubiquitin protein ligase E3A (human papilloma virus E6- 
               
               
                 associated protein, Angelman syndrome) (UBE3A), transcript variant 3; 
               
               
                 NM_138340.3| Homo sapiens  abhydrolase domain containing 3 (ABHD3); 
               
               
                 NM_144617.1| Homo sapiens  heat shock protein, alpha-crystallin-related, B6 (HSPB6); 
               
               
                 NM_145013.1| Homo sapiens  hypothetical protein MGC35558 (MGC35558); 
               
               
                 NM_145341.2| Homo sapiens  programmed cell death 4 (neoplastic transformation inhibitor) 
               
               
                 (PDCD4), transcript variant 2; 
               
               
                 NM_146388.1| Homo sapiens  mitochondrial ribosomal protein L4 (MRPL4), nuclear gene 
               
               
                 encoding mitochondrial protein, transcript variant 3; 
               
               
                 NM_147193.1| Homo sapiens  GLIS family zinc finger 1 (GLIS1); 
               
               
                 NM_152643.5| Homo sapiens  kinase non-catalytic C-lobe domain (KIND) containing 1 
               
               
                 (KNDC1), transcript variant 1; 
               
               
                 NM_153355.2| Homo sapiens  T-cell lymphoma breakpoint associated target 1 (TCBA1); 
               
               
                 NM_153613.1| Homo sapiens  PLSC domain containing protein (LOC254531); 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
             
           
               
                 TABLE 18 
               
             
             
               
                   
               
               
                 BISULFITE SEQUENCING OF NORMAL LUNG AND 
               
               
                 TUMOR DNA 
               
             
          
           
               
                 Name 
                 CpG island nucleotides 
                 Normals 
                 Tumor 
               
               
                   
               
               
                 PHKA2 
                 BS1 (460-620) 
                 NORMAL UM 
                 TUMOR UM 
               
               
                 CBR3 
                 BS1 (841-961) 
                 NORMAL UM 
                 TUMOR UM 
               
               
                 CAMK4 
                 BS1 (441-706) 
                 NORMAL M 
                 TUMOR UM 
               
               
                 HOXB5 
                 BS1 (673-782) 
                 NORMAL UM 
                 TUMOR UM 
               
               
                 PAK3 
                 BS1 (602-1115) 
                 normal UM 
                 Tumor M 
               
               
                 ZNF198 
                 BS1 (10-220) 
                 NORMAL UM 
                 TUMOR UM 
               
               
                 PIGH 
                 BS1 (680-888) 
                 NORMAL UM 
                 TUMOR M 
               
               
                 RGS4 
                 BS1 (904-1149) 
                 NORMAL UM 
                 TUMOR UM 
               
               
                 TUBB4 
                 BS1 (428-694) 
                 NORMAL UM 
                 TUMOR M 
               
               
                 NISCH 
                 BS2 (315-569) 
                 NORMAL UM 
                 TUMOR M 
               
               
                 RBM15B 
                 BS1 (883-1111) 
                 NORMAL M 
                 TUMOR M 
               
               
                 ARFGAP3 
                 BS1 (505-666) 
                 NORMAL M 
                 TUMOR M 
               
               
                   
               
               
                 UM = unmethylated; 
               
               
                 M = methylated; 
               
               
                 BS1 = first CpG; 
               
               
                 BS2 = second CpG 
               
             
          
         
       
     
         [0000]    
       
         
               
             
           
               
                 TABLE 19 
               
               
                   
               
             
             
               
                 
                   
                             
                     
                         
                         
                     
                   
                 
               
               
                   
               
               
                 
                   
                             
                     
                         
                         
                     
                   
                 
               
               
                   
               
               
                 
                   
                             
                     
                         
                         
                     
                   
                 
               
               
                   
               
               
                 
                   
                             
                     
                         
                         
                     
                   
                 
               
               
                   
               
               
                 
                   
                             
                     
                         
                         
                     
                   
                 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
               
               
               
             
               
               
               
               
               
               
               
             
           
               
                 TABLE 20 
               
             
             
               
                   
               
               
                 02 10 06 
               
               
                 Percent of methylated cases tested (%) 
               
             
          
           
               
                   
                   
                 cell line 
                   
                   
                   
                 Cancer-specific 
               
               
                   
                 Name 
                 Methylation 
                 Method 
                 Tissues N 
                 Tissues T 
                 Methylation 
               
               
                   
                   
               
             
          
           
               
                 1 
                 B4GALT1 
                 M 
                 MSP 
                 * 
                 * 
                   
               
               
                 2 
                 C10orf119 
                 M 
                 SEQ 
                 0 
                 0 
               
               
                 3 
                 C19orf13 
                 M 
                 SEQ 
                 0 
                 0 
               
               
                 4 
                 CBR1 
                 M 
                   
                 * 
                 * 
               
               
                 5 
                 COPS4 
                 M 
                   
                 * 
                 * 
               
               
                 6 
                 COVA1 
                 M 
                   
                 * 
                 * 
               
               
                 7 
                 CSRP1 
                 M 
                 SEQ 
                 90 
                 50 
               
               
                 8 
                 DARS 
                 M 
                 SEQ 
                 40 
                 22 
               
               
                 9 
                 DNAJC10 
                 M/U 
                 SEQ 
                 0 
                 0 
               
               
                 10 
                 FKBP14 
                 M 
                 SEQ 
                 40 
                 50 
               
               
                 11 
                 FN3KRP 
                 M 
                   
                 * 
                 * 
               
               
                 12 
                 GANAB 
                 M 
                   
                 * 
                 * 
               
               
                 13 
                 GPR116 
                 M 
                 SEQ 
                 0 
                 90 
                 ✓ 
               
               
                 14 
                 HUS1 
                 M 
                 SEQ 
                 0 
                 22 
               
               
                 15 
                 KLF11 
                 M 
                 SEQ 
                 100 
                 100 
               
               
                 16 
                 MRPL4 
                 M 
                   
                 * 
                 * 
               
               
                 17 
                 MYLK 
                 M 
                 SEQ 
                 0 
                 10 
               
               
                 18 
                 NELF 
                 M 
                 SEQ 
                 66 
                 90 
               
               
                 19 
                 NETO2 
                 M 
                   
                 * 
                 * 
               
               
                 20 
                 OSMR 
                 M 
                 SEQ 
                 33 
                 100 
                 ✓ 
               
               
                 21 
                 PAPSS2 
                 M 
                 SEQ 
                 100 
                 100 
               
               
                 22 
                 PC4 
                 M 
                 SEQ 
                 0 
                 44 
                 ✓ 
               
               
                 23 
                 RBMS2 
                 M 
                 SEQ 
                 100 
                 100 
               
               
                 24 
                 RHOB 
                 M 
                   
                 * 
                 * 
               
               
                 25 
                 SECTM1 
                 M 
                   
                 * 
                 * 
               
               
                 26 
                 SIRT2 
                 M 
                 SEQ 
                 100 
                 100 
               
               
                 27 
                 SIRT7 
                 M 
                   
                 * 
                 * 
               
               
                 28 
                 SLC35D1 
                 M 
                 SEQ 
                 0 
                 0 
               
               
                 29 
                 SLC39A4 
                 M 
                 SEQ 
                 11 
                 66.6 
                 ✓ 
               
               
                 30 
                 SLC9A3R1 
                 M 
                   
                 * 
                 * 
               
               
                 31 
                 TTRAP 
                 M 
                   
                 * 
                 * 
               
               
                 32 
                 TUBG2 
                 M 
                 SEQ 
                 100 
                 100 
               
               
                 33 
                 UBE2I 
                 M 
                 SEQ 
                 0 
                 50 
                 ✓ 
               
               
                 34 
                 UBE3A 
                 M 
                 SEQ 
                 0 
                 100 
                 ✓ 
               
               
                 35 
                 FLJ20277 
                 M 
                 SEQ 
                 100 
                 100 
               
               
                 36 
                 MYBL2 
                 M 
                 SEQ 
                 70 
                 100 
               
               
                   
               
               
                 N; paired normal tissues, 
               
               
                 T; paired colon cancer tissues 
               
               
                 ✓; cancer-specific methylation, 
               
               
                 *: bad results