Patent Publication Number: US-2004048279-A1

Title: Method for detecting methylation states for a toxicological diagnostic

Description:
FIELD OF THE INVENTION  
       [0001] The levels of observation that have been well studied in molecular biology according to developments in methods in recent years include the genes themselves, the transcription of these genes into RNA and the translation to proteins therefrom. During the course of development of an individual, which gene is turned on and how the activation and inhibition of certain genes in certain cells and tissues are controlled can be correlated with the extent and nature of the methylation of the genes or of the genome. In this regard, pathogenic states are also expressed by a modified methylation pattern of individual genes or of the genome.  
       [0002] In the present invention, the methylation states of toxicologically relevant genes and the data determined thereby are combined to form methylation patterns. By comparison of the patterns obtained with appropriate reference samples, comprehensive prognostic information on the toxicological properties of substances can be made. In addition, a method will be presented, which makes possible to a great extent the analysis of methylation positions of the genes to be investigated.  
       PRIOR ART  
       [0003] The toxicological evaluation of chemical substances is currently being conducted in particular by experiments on animals. Animal experiments are ethically problematical, time-consuming and expensive. In order to be better able to estimate the toxicological consequences of substances, methods of analyzing gene expression are increasingly utilized. Such approaches were previously essentially based on the analysis of mRNA. In particular, thousands of genes can be investigated in parallel with DNA chips for changes in their transcriptional activity. Specific toxicological parameters can be concluded from the modified gene expression (Stoughton R. et al., U.S. Pat. No. 6,132,969).  
       [0004] 5-Methylcytosine is the most frequent covalently modified base in the DNA of eukaryotic cells. For example, it plays a role in the regulation of transcription, in genetic imprinting and in tumorigenesis. The identification of 5-methylcytosine as a component of genetic information is thus of considerable interest. 5-Methylcytosine positions, however, cannot be identified by sequencing, since 5-methylcytosine has the same base-pairing behavior as cytosine. In addition, in the case of a PCR amplification, the epigenetic information which is borne by the 5-methylcytosines is completely lost.  
       [0005] A relatively new method that in the meantime has become the most widely used method for investigating DNA for 5-methylcytosine is based on the specific reaction of bisulfite with cytosine, which, after subsequent alkaline hydrolysis, is then converted to uracil, which corresponds in its base-pairing behavior to thymidine. In contrast, 5-methylcytosine is not modified under these conditions. Thus, the original DNA is converted so that methylcytosine, which originally cannot be distinguished from cytosine by its hybridization behavior, can now be detected by “standard” molecular biology techniques as the only remaining cytosine, for example, by amplification and hybridization or sequencing. All of these techniques are based on base pairing, which is now fully utilized. The prior art, which concerns sensitivity, is defined by a method that incorporates the DNA to be investigated in an agarose matrix, so that the diffusion and renaturation of the DNA is prevented (bisulfite reacts only on single-stranded DNA) and all precipitation and purification steps are replaced by rapid dialysis. (Olek, A. et al., Nucl. Acids Res. 1996, 24, 5064-5066). Individual cells can be investigated by this method, which illustrates the potential of the method. Of course, up until now, only individual regions of up to approximately 3000 base pairs long have been investigated; a global investigation of cells for thousands of possible methylation analyses is not possible. Of course, this method also cannot reliably analyze very small fragments of small quantities of sample. These are lost despite the protection from diffusion through the matrix.  
       [0006] An overview of other known possibilities for detecting 5-methylcytosines can be derived from the following review article: Rein, T., DePamphilis, M. L., Zorbas, H., Nucleic Acids Res. 1998, 26, 2255.  
       [0007] The bisulfite technique has been previously applied only in research, with a few exceptions (e.g., Zechnigk, M. et al., Eur. J. Hum. Gen. 1997, 5, 94-98). However, short, specific segments of a known gene have always been amplified after a bisulfite treatment and either completely sequenced (Olek, A. and Walter, J., Nat. Genet. 1997, 17, 275-276) or individual cytosine positions are detected by a “primer extension reaction” (Gonzalgo, M. L. and Jones, P. A., Nucl. Acid Res. 1997, 25, 2529-2531, WO-Patent 95-00669) or an enzyme step (Xiong, Z. and Laird, P. W., Nucl. Acids Res. 1997, 25, 2532-2534). Detection by hybridization has also been described (Olek et al., WO-A 99-28,498).  
       [0008] Other publications which are concerned with the application of the bisulfite technique for the detection of methylation in the case of individual genes are: Xiong, Z. and Laird, P. W. (1997), Nucl. Acids Res. 25, 2532; Gonzalgo, M. L. and Jones, P. A. (1997), Nucl. Acids Res. 25, 2529; Grigg, S. and Clark, S. (1994), Bioassays 16, 431; Zeschnik, M. et al. (1997), Human Molecular Genetics 6, 387; Teil, R. et al. (1994), Nucl. Acids Res. 22, 695; Martin, V. et al. (1995), Gene 157, 261; WO-A 97-46,705, WO 95-15,373 and WO 45,560.  
       [0009] A review of the prior art in oligomer array production can be taken from a special edition of Nature Genetics that appeared in January 1999 (Nature Genetics Supplement, Volume 21, January 1999) and the literature cited therein.  
       [0010] Probes with multiple fluorescent labels have been used for scanning an immobilized DNA array. Particularly suitable for fluorescent labels is the simple introduction of Cy3 and Cy5 dyes at the 5-OH of the respective probe. The fluorescence of the hybridized probes is detected, for example, by means of a confocal microscope. The dyes Cy3 and Cy5, among many others, are commercially available.  
       [0011] Matrix-assisted laser desorptions/ionization mass spectrometry (MALDI-TOF) is a very powerful development for the analysis of biomolecules (Karas, M. and Hillenkamp, F. (1988), Laser desorption ionization of proteins with molecular masses exceeding 10000 daltons. Anal. Chem. 60: 2299-2301). An analyte is embedded in a light-absorbing matrix. The matrix is vaporized by a short laser pulse and the analyte molecule is transported unfragmented into the gaseous phase. The analyte is ionized by collisions with matrix molecules. An applied voltage accelerates the ions in a field-free flight tube. Ions are accelerated to varying degrees based on their different masses. Smaller ions reach the detector sooner than large ions.  
       [0012] Genomic DNA is obtained from DNA of cells, tissue or other test samples by standard methods. This standard methodology is found in references such as Fritsch and Maniatis, eds., Molecular Cloning: A Laboratory Manual, 1989.  
       [0013] At present, it is not state of the art to investigate large quantities of samples relative to more important methylation positions for toxicological diagnosis.  
       PRESENTATION OF THE PROBLEM  
       [0014] The present invention will present a method, which is suitable for the diagnosis of methylation states of genes with toxicological relevance. The invention is based on the knowledge that cytosine methylation states are particularly suitable for the diagnosis of changes in the expression of genes with toxicological relevance.  
       DESCRIPTION  
       [0015] The present invention describes a method for evaluating toxicological properties of specific substances. The method is based on the detection of specific changes in the methylation state or methylation pattern of genomic DNA, which [changes] occur due to the substance being tested.  
       [0016] A methylation state in this invention is a state of methylation of cytosine bases that is specific for a DNA sample.  
       [0017] A sample that contains the DNA of an organism or a cell culture, which [sample] has been derived from this organism or cell culture, was previously subjected to a substance to be tested for its toxicological effect.  
       [0018] The genomic DNA to be analyzed is thus preferably obtained from the usual sources for DNA, such as, e.g., cell lines, blood, sputum, stool, urine, cerebrospinal fluid, tissue embedded in paraffin, for example tissue from eyes, intestine, kidney, brain, heart, prostate, lungs, breast or liver, histological slides and all possible combinations thereof.  
       [0019] In a first step of the method, the DNA that is obtained is treated in such a way that methylated cytosine bases produce a different base sequence in said DNA. Then the base sequence of said treated DNA sample is determined and a conclusion is made of a methylation state or a methylation pattern that is characteristic for the sample. Finally, by comparison of the methylation state or methylation pattern obtained with the methylation states or methylation patterns of other samples, a conclusion can be made of the effect of the substance used on the organism or cell culture and/or the effects of different substances can be compared with one another.  
       [0020] Preferably, in the first step of the method, a genomic DNA sample is chemically treated in such a way that cytosine bases that are unmethylated at the 5′-position are converted to uracil, thymine or another base unlike cytosine in its hybridization behavior. In the following, this is understood as chemical pretreatment.  
       [0021] The above-described treatment of genomic DNA with bisulfite (hydrogen sulfite, disulfite) and subsequent alkaline hydrolysis, which leads to a conversion of unmethylated cytosine nucleobases to uracil is preferred for this purpose.  
       [0022] In the second step of the method, the base sequence of a part of the chemically treated DNA is determined and a conclusion is made of the methylation states characteristic of the sample.  
       [0023] Preferably, in a second step of the method, fragments of the chemically pretreated genomic DNA are first amplified with the use of primer oligonucleotides. Preferably, more than 10 different fragments, which are 100-2000 base pairs long, are amplified.  
       [0024] In a preferred variant of the method, the amplification is preferably conducted by means of the polymerase chain reaction (PCR), wherein a heat-stable DNA polymerase is preferably used.  
       [0025] It is preferred according to the invention that the amplification of several DNA segments is conducted in one reaction vessel.  
       [0026] In a preferred variant of the method, the set of primer oligonucleotides comprises at least two oligonucleotides, each of whose sequences is inversely complementary or identical to a segment that is at least 18 base pairs long of the sequences of the genes to be investigated. The primer oligonucleotides are preferably characterized in that they do not contain a CpG dinucleotide.  
       [0027] Preferably, at least one of the two primer oligonucleotides used for amplifying a specific segment of the chemically pretreated DNA contains identifiable labels.  
       [0028] It is preferred according to the invention that the labels of the amplificates are fluorescent labels.  
       [0029] It is preferred according to the invention that the labels of the amplificates are radionuclides.  
       [0030] It is preferred according to the invention that the labels of the amplificates are removable molecular fragments with typical masses, which are detected in a mass spectrometer.  
       [0031] According to the invention, it is preferred that the amplificates, fragments of the amplificates or probes that are complementary to the amplificates, are detected in the mass spectrometer.  
       [0032] It is preferred according to the invention that the produced fragments have a single positive or single negative net charge for better detectability in the mass spectrometer.  
       [0033] It is preferred according to the invention that the detection is carried out and visualized by means of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) or by means of electrospray mass spectrometry (ESI).  
       [0034] It is preferred according to the invention that at least one primer oligonucleotide is bound to a solid phase in the amplification.  
       [0035] Preferably, the probe oligonucleotides or PNA oligomers are bound to defined sites of a solid phase.  
       [0036] According to the invention it is further preferred that different oligonucleotide and/or PNA oligomer sequences are arranged on a planar solid phase in the form of a rectangular or hexagonal grid.  
       [0037] The solid-phase surface is preferably comprised of silicon, glass, polystyrene, aluminum, steel, iron, copper, nickel, silver, or gold.  
       [0038] In the third step of the method, the amplificates are hybridized to a set of at least 10 oligonucleotide or PNA oligomer probes. The amplificates thus serve as samples, which hybridize to the oligonucleotides previously bound to a solid phase. In the sense of this invention, hybridization is to be understood as a binding with the formation of a duplex structure of an oligonucleotide to a completely complementary sequence in the sense of a Watson-Crick base pairing in the sample DNA. The unhybridized fragments are then removed.  
       [0039] Said oligonucleotides comprise at least one base sequence with a length of 13 nucleotides, which is inversely complementary or identical to a segment of the base sequences of the genes to be investigated. The cytosine of the CpG dinucleotide is the 5th to 9th nucleotide viewed from the 5′-end of the 13-mer. One oligonucleotide is present for each CpG dinucleotide.  
       [0040] Said PNA oligomers comprise at least one base sequence with a length of 9 nucleotides, which is inversely complementary or identical to a segment of the base sequences of the genes to be investigated, which contains at least one CpG dinucleotide. The cytosine of the CpG dinucleotide is the 4th to 6th nucleotide viewed from the 5′-end of the 9-mer. One oligonucleotide is present for each CpG dinucleotide.  
       [0041] In the fourth step of the method, the unhybridized amplificates are removed.  
       [0042] In the last step of the method, the hybridized amplificates are detected.  
       [0043] It is preferred according to the invention that labels which are introduced on the amplificates at any position of the solid phase at which an oligonucleotide sequence is found, can be identified. The use of a method for the diagnosis of methylation states within a group of genes, which are characterized by a particularly well-documented association with toxicological processes, is preferred according to the invention.  
       [0044] The method preferably serves for the diagnosis and/or prognosis of adverse events for patients or individuals, whereby these adverse events are related to the diagnosis of toxicologically important parameters.  
       [0045] According to the invention, the method is used for the diagnosis and/or prognosis of adverse events for patients or individuals, whereby these adverse events are related to the diagnosis of toxicologically important parameters.  
       [0046] The set of genes to be investigated comprises at least one of the genes listed in Table 1 or, however, sequences which are identical, or at least 85% homologous in the region of the exon, to the genes listed in Table 1.  
                                       GenBank       Gene Name   Accession #(s)                  serotransferrin precursor; siderophilin; beta-1-metal binding globulin   M12530       lactotransferrin precursor; lactoferrin   X53961       apolipoprotein E precursor (APOE)   M12529       lipopolysaccharide-binding protein precursor (LBP)   M35533       B-lymphocyte kinase; tyrosine-protein kinase BLK; p55-BLK   Z33998       apolipoprotein A-I precursor (APOAI)   X00566       apolipoprotein A-II precursor (APOAII)   X00955       apolipoprotein C-III precursor (APOCIII)   X01388       endothelin 1 (ET1)   Y00749       macrophage colony stimulating factor 1 (CSF1; MCSF)   M37435       familial intrahepatic cholestasis 1 protein (FIC1)   AF038007       vascular endothelial growth factor D (VEGFD); C-FOS-induced growth factor (FIGF)   D89630       complement component 4-binding protein alpha (C4B-binding protein; C4BPA);       proline-rich protein (PRP)   M31452       insulin-like growth factor II (IGF2); somatomedin A   M29645       granulocyte-macrophage colony stimulating factor (GM-CSF); CSF2   M11220       epidermal growth factor precursor (EGF); beta-urogastrone   X04571       hepatocyte growth factor activator (HGF activator)   D14012       macrophage inflammatory protein 1 beta precursor (MIP1-beta);       T-cell activation protein 2 (AT2); PAT 744; H400; SIS-gamma;       lymphocyte activation gene 1 protein (LAG 1); HC21;       small inducible cytokine A4 (SCYA4); G 26 T-lymphocyte secreted protein   J04130       glial growth factor 2 precursor (GGFHPP2); neuregulin; heregulin-beta3 + neu       differentiation factor + heregulin-alpha   L12260;           L12261 +           U02326 + M94165       T-cell-specific rantes protein precursor; sis delta; small inducible cytokine A5 (SCYA5);       rantes pro-inflammatory cytokine   M21121       macrophage inflammatory protein 1 alpha precursor (MIP1-alpha);       tonsillar lymphocyte LD78 alpha protein; G0S19-1 protein; PAT 464.2; SIS-beta;       small inducible cytokine A3 (SCYA3)   M23452       oncostatin M (OSM)   M27288       insulin-like growth factor binding protein 1 (IGFBP1); placental protein 12 (PP12)   M31145       vascular endothelial growth factor precursor (VEGF);       vascular permeability factor (VPF)   M32977; M27281       hepatocyte growth factor (HGF); scatter factor (SF); hepatopoeitin A   M60718       thymosin beta-10 (TMSB10; THYB10); PTMB10   M92381       interferon gamma-induced protein precursor (gamma-IP10)   X02530       macrophage inflammatory protein 2 alpha (MIP2-alpha);       growth-regulated protein beta (GRO-beta)   X53799       OX40 ligand (OX40L); GP34; tax-transcriptionally activated glycoprotein 1 (TXGP1)   X79929       transforming growth factor-beta 3 (TGF-beta3)   J03241       delta-like protein precursor (DLK)   U15979; Z12172       insulin-like growth factor IA precursor (IGF1A); IGFBP1;       somatomedin C + insulin-like growth factor I (IGF1)   M27544 + M37484       CC chemokine eotaxin precursor; eosinophil chemotactic protein;       small inducible cytokine A11 (SCYA11)   D49372;           Z75669; Z75668       sonic hedgehog (SHH)   L38518       interleukin-1 receptor antagonist protein precursor (IL-1RA; IRAP)   M63099       macrophage inhibitory cytokine 1 (MIC1)   AF019770       erythropoietin   M11319       eosinophil granule major basic protein precursor (MBP);       pregnancy-associated major basic protein; bone marrow proteoglycan 2   Y00809       insulin-like growth factor-binding protein 3 precursor       (IGF-binding protein 3; IGFBP3; IBP3)   M31159; M35878       cellular retinoic acid-binding protein II (CRABP2)   M68867       corticoliberin precursor; corticotropin-releasing factor (CRF);       corticotropin releasing hormone (CRH)   V00571       interferon gamma precursor (IFN-gamma; IFNG); immune interferon   X01992; M29383       interleukin-2 precursor (IL-2); T-cell growth factor (TCGF)   A14844       interleukin-1 alpha precursor (IL-1 alpha; IL1A); hematopoietin-1   X02851       interleukin-4 precursor (IL-4); B-cell stimulatory factor 1 (BSF-1);       lymphocyte stimulatory factor 1   M13982       interleukin-6 precursor (IL-6); B-cell stimulatory factor 2 (BSF2);       interferon beta-2 (IFNB2); hybridoma growth factor   X04602; M14584       interleukin-5 precursor (IL-5); T-cell replacing factor (TRF);       eosinophil differentiation factor; B-cell differentiation factor I   X04688; J03478       interleukin-12 beta subunit precursor (IL-12B);       cytotoxic lymphocyte maturation factor 40-kDa subunit (CLMF p40);       NK cell stimulatory factor subunit 2 (NKSF2)   M65290       interleukin-12 alpha subunit precursor (IL-12A);       cytotoxic lymphocyte maturation factor 35-kDa subunit (CLMF p35);       NK cell stimulatory factor subunit 1 (NKSF1)   M65291       pancreatitis-associated protein 1 precursor   D13510       alpha-1-acid glycoprotein 1 precursor (AGP1); orosomucoid 1 (OMD1)   X02544       C-reactive protein precursor   X56692       corticosteroid-binding globulin   J02943       prostaglandin-endoperoxide synthase 1 precursor; prostaglandin G/H synthase 1       (PGH synthase 1; PTGS1; PHS1); cyclooxygenase 1 (COX1)   M59979       amphiphysin (AMPH)   U07616       5-hydroxytryptamine 1D receptor (5-HT-1D; HTR1D); serotonin receptor   M89955       neuromedin B precursor   M21551       major prion protein precursor (PRP); PRP27-30; PRP33-35C; ASCR   M13667       dopamine beta-hydroxylase (DBH); dopamine-beta-monooxygenase precursor   X13255       Alzheimer&#39;s disease amyloid A4 protein precursor; protease nexin-II (PN-II); APPI   Y00264       membrane-bound &amp; soluble catechol-O-methyltransferase (COMT)   M65212       flavin-containing amine oxidase A; monoamine oxidase (MAO-A)   M68840       erythropoietin receptor (EPOR)   M60459       cation-independent mannose-6-phosphate receptor precursor       (CI man-6-P receptor; CI-MPR);       insulin-like growth factor II receptor (IGFR II)   Y00285; J03528       activin receptor type II precursor (ACTRIIA; ACVR2)   D31770       RETINOID X RECEPTOR GAMMA (RXR-GAMMA)   U38480       transcriptional enhancer factor (TEF1); protein GT-IIC; transcription factor 13 (TCF13)   M63896       glucocorticoid receptor (GRL)   M10901       orphan nuclear hormone receptor BD73   L31785       low-density lipoprotein receptor (LDL receptor; LDLR)   M28219       sulfonylurea receptor 2A (SUR2A)   AF061323       sulfonylurea receptor (SUR);       ATP-binding cassette subfamily C (CFTR/MRP) member 8 (ABCC8)   L78207       farnesol receptor HRR-1   U68233       tyrosine protein kinase receptor UFO   X66029       colorectal cancer suppressor protein precursor (DCC)   X76132       vascular cell adhesion protein 1   X53051       alpha1 catenin (CTNNA1); cadherin-associated protein;       alpha E-catenin   D13866; D14705;           L23805; L22080       integrin alpha 9 (ITGA9); integrin alpha-RLC   D25303; L24158       intercellular adhesion molecule 1 precursor (ICAM1); major group rhinovirus receptor;       CD54 antigen   J03132       ras-related protein RAB5A   M28215       E-selectin precursor (SELE); endothelial leukocyte adhesion molecule 1 (ELAM1);       leukocyte-endothelial cell adhesion molecule 2 (LECAM2); CD62E antigen   M30640       NADH-ubiquinone dehydrogenase 1 beta subcomplex 7 18-kDa subunit (NDUFB7);       complex I-B18 (CI-B18); cell adhesion protein SQM1   M33374       neural-cadherin precursor (N-cadherin; NCAD);       cadherin 2 (CDH2)   M34064; X57548;           X54315; S42303       cell surface adhesion glycoproteins LFA-1/CR3/p150,95 beta-subunit precursor;       LYAM1; integrin beta 2 (ITGB2); CD18 antigen; complement receptor C3 beta subunit   M15395       fibronectin receptor alpha subunit (FNRA); integrin alpha 5 (ITGA5); VLA5;       CD49E antigen   X06256       fibronectin receptor beta subunit (FNRB); integrin beta 1 (ITGB1);       very late antigen 4 beta subunit (VLA4); CD29 antigen   X07979       integrin alpha L (ITGAL); leukocyte adhesion glycoprotein alpha subunit precursor;       leukocyte function-associated molecule 1 alpha chain (LFA1); CD11A antigen   Y00796       cadherin 6 precursor (CDH6); kidney cadherin (K-cadherin)   D31784       cadherin 11 precursor (CDH11); osteoblast-cadherin (OB-cadherin); OSF4   L34056       cadherin 12 (CDH12); brain cadherin precursor (Br-cadherin);       neural cadherin 2 (N-cadherin 2)   L34057; L33477       cadherin 13 (CDH13); truncated cadherin precursor (T-cadherin);       heart cadherin (H-cadherin)   L34058;           U59289; U59288       cadherin 3 (CDH3); placental cadherin precursor (P-cadherin; CDHP)   X63629       GAP JUNCTION ALPHA-5 PROTEIN (CONNEXIN 40) (CX40)   L34954       INVOLUCRIN   M13903       fibrinogen G gamma polypeptide   X51473;           X02415 K02569       plasma-cell membrane glycoprotein PC-1; alkaline phosphodiesterase I;       nucleotide pyrophosphatase (NPPase)   M57736       annexin V; lipocortin V; endonexin II; calphobindin I (CBP-I);       placental anticoagulant protein I (PAP-I); PP4; thromboplastin inhibitor;       vascular anticoagulant-alpha (VAC-alpha; anchorin CII   X12454       laminin alpha 1 subunit precursor (LAMA1); laminin A chain   X58531       intestinal fatty acid-binding protein 2 (FABP2; IFABP)+       liver fatty acid-binding protein 1 (FABP1; LFABP)   M10050 + M10617       sodium-independent organic anion transporter;       organic anion transporting polypeptide (OATP); SLC21A3   U21943       polyspecific organic cation transporter N1 (OCTN1)   AB007448       TNF-alpha-stimulated ABC protein (TSAP)   AF027302       organic cation transporter-like protein 2 (ORCTL2)   AF037064       organic cation transporter N2 (OCTN2)   AF057164       MRP/organic anion transporter (MOAT-B)   AF071202       adrenoleukodystrophy-related protein (ALDR)   AJ000327       skeletal muscle adenine nucleotide translocator 1 (ANT1);       heart/skeletal muscle ADP/ATP carrier protein isoform T1;       ADP/ATP translocase 1   J02966       down-regulated in adenoma protein (DRA)   L02785       mitochondrial uncoupling protein 3 (UCP3)   AF011449       mitochondrial carnitine palmitoyltransferase II precursor (CPTase; CPT2)   M58581       mitochondrial brown fat uncoupling protein 1 (UCP1)   U28480       prostaglandin transporter (PGT); solute carrier family 21 member 2 (SLC21A2)   U70867       mitochondrial uncoupling protein 2 (UCP2); UCPH   U82819       bile salt export pump (BSEP)   AF091582       anthracycline resistance-associated protein (ARA)   X95715       kidney organic cation transporter   X98333       multidrug resistance-associated protein 3 (MRP3); MLP2; ABCC3   Y17151       antigen peptide transporter 2 (APT2); peptide supply factor 2 (PSF2);       peptide transporter involved in antigen processing 2 (TAP2);       ATP-binding cassette subfamily B (MBR/TAP) member 3 (ABCC3);       HLA class II histocompatibility antigen DO beta chain precursor   X66401;           L09191; L10287       putative renal organic anion transporter 1 (hROAT1)   AF057039       chloride conductance regulatory protein ICLN; nucleotide-sensitive chloride channel 1A;       chloride ion current inducer protein (CLCI); reticulocyte PICLN   X91788       neutral amino acid transporter A (SATT);       alanine/serine/cysteine/threonine transporter (ASCT1)   L14595       monocarboxylate transporter 1 (MCT1)   L31801       ileal sodium-dependent bile acid transporter (ISBT);       ileal sodium/taurocholate cotransporting polypeptide (NTCP2); SLC10A2   U10417       sodium-dependent bile acid cotransporter;       hepatic sodium/taurocholate cotransporting polypeptide (NTCP); SLC10A1   L21893       sodium- &amp; chloride-dependent glycine transporter 1 (GLYT-1)   S70609       cystic fibrosis transmembrane conductance regulator (CFTR);       cAMP- dependent chloride channel   M28668       canalicular multispecific organic anion transporter;       multidrug resistance-associated protein 2 (MRP2);       canalicular multidrug resistance protein   U63970       organic cation transporter 1   U77086       GAP JUNCTION BETA-1 PROTEIN (CONNEXIN 32)       (CX32) (LIVER GAP JUNCTION PROTEIN)   X04325       cadherin1 (CDH1); epithelial cadherin precursor (E-cadherin; CDHE);       uvomorulin (UVO); CAM 120/80   Z13009       smoothened; GX   U84401       ephrin type-A receptor 2 precursor; epithelial cell kinase (ECK);       tyrosine-protein kinase receptor ECK   M59371 M36395       NADPH-cytochrome p450 reductase   S90469       NCK melanoma cytoplasmic src homolog (HSNCK)   X17576       JV18-1. HMAD-2 OR MADR2 OR SMAD2   U68018       dual-specificity mitogen-activated protein kinase kinase 1 (MAP kinase kinase 1;       MAPKK 1; MKK1); extracellular signal-regulated kinase 1;       ERK activator kinase 1   L05624       c-jun N-terminal kinase 1 (JNK1); JNK46   L26318       mitogen-activated protein kinase p38 (MAP kinase p38);       cytokine suppressive anti-inflammatory drug-binding protein       (CSAID binding protein; CSBP); MAX-interacting protein 2 (MXI2)   L35253; L35263       protein kinase C beta I (PKC-beta-1)   M27545; X06318       mitogen-activated protein kinase 9 (MAP kinase 9; MAPK9; PRKM9);       c-jun N-terminal kinase 2 (JNK2); JNK55   L31951       C-jun N-terminal kinase 3 alpha2 (JNK3A2);    U34819 + U07620       PRKM10 + MAP kinase p493F12       dual-specificity mitogen-activated protein kinase kinase 6       (MAP kinase kinase 6; MAPKK 6; MKK6); MAPK/ERK kinase 6; SAPKK3   U39657       p21-activated kinase gamma (PAK-gamma; PAK2); PAK65; S6/H4 kinase   U24153       mitogen-activated protein kinase P38 beta (MAP kinase P38 beta);       stress-activated protein kinase 2 (SAPK2)   U53442       MAPK/ERK kinase kinase 3 (MEK kinase 3; MEKK3)   U78876       dual specificity mitogen-activated protein kinase kinase 2       (MAP kinase kinase 2; MAPKK 2); ERK activator kinase 2;       MAPK/ERK kinase 2 (MEK2)   L11285       dual specificity mitogen-activated protein kinase kinase 5        (MAP kinase kinase 5; MAPKK 5)   U25265       ribosomal protein S6 kinase II alpha 1 (S6KII-alpha 1);   L07597       ribosomal S6 kinase 1 (RSK1)       B-lymphocyte germinal center kinase (GC kinase)   U07349       YSK1; Ste20 &amp; SPS1-related kinase   D63780       protein phosphatase 2B regulatory subunit;   M30773       calcineurin B subunit isoform 1       protein-tyrosine phosphatase MEG2 (PTPASE-MEG2)   M83738       protein-tyrosine phosphatase alpha precursor   M34668       (R-PTP-alpha; PTPRA; PTPA)       ras associated with diabetes (RAD1)   L24564       CDC42 homolog; G25K GTP-binding protein       (brain isoform + placental isoform)   M35543 + M57298       calmegin   D86322       calbindin; avian-type vitamin D-dependent calcium binding protein (CABP); D-28K   X06661       stratifin (SFN); 14-3-3 protein sigma; epithelial cell marker protein 1; HME1   AF029082       FKBP-rapamycin associated protein (FRAP); rapamycin target protein   L34075       zinc finger protein 37 (ZFP37); KRAB domain zinc finger protein   AF022158       CCAAT/enhancer-binding protein epsilon (C/EBP epsilon; CEBPE)   U48866; U48865       transcription initiation factor IID; TATA-box factor;       TATA sequence-binding protein (TBP)   M34960       60S ribosomal protein L6 (RPL6);   (TAXREB107);       TAX-responsive enhancer element binding protein 107       neoplasm-related protein C140   X69391       DNA-binding protein HIP116; ATPase; SNF2/SWI2-related protein   L34673       basic transcription factor 2 44-kDa subunit (BTF2p44)   Z30094       octamer-binding transcription factor 2 (oct-2; OTF2); lymphoid-restricted       immunoglobulin octamer binding protein NF-A2; POU2F2   M36542       zinc finger protein 40 (ZNF40); human immunodeficiency virus type I       enhancer-binding protein 1 (HIV-EP1);       major histocompatibility complex binding protein 1 (MBP-1);       positive regulatory domain II binding factor 1 (PRDII-BF1)   X51435       nervous-system specific octamer-binding transcription factor N-oct3;       N-oct5A &amp; N-oct5B; brain-specific homeobox/       POU domain protein 2 (POU3F2);       brn2; oct7   Z11933       hypoxia-inducible factor 1 alpha (HIF1 alpha); ARNT-interacting protein;       member of PAS protein 1 (MOP1)   U22431       CCAAT/enhancer binding protein alpha (C/EBP alpha)   U34070       HOMEOBOX PROTEIN MOX-2 (GROWTH ARREST-SPECIFIC HOMEOBOX)   X82629       endothelial transcription factor GATA2   M68891       DNA-binding protein inhibitor Id-2   M97796       activating transcription factor 4 (ATF4);       tax-responsive enhancer element B67 (TAXREB67);       cAMP-response element-binding protein 2 (CREB2)   D90209       heat shock factor protein 1 (HSF1); heat shock transcription factor 1 (HSTF1); TCF5   M64673       FK506-binding protein 13 precursor (FKBP13);       FKBP2; peptidyl-prolyl cis-trans isomerase (PPIase)   M65128       cAMP response element binding protein (CRE-BP1); transcription factor ATF2; HB16   M31630       cAMP-response element binding protein (CREB)   M34356       early growth response protein 1 (EGR1); transcription factor ETR103; KROX24;       zinc finger protein 225 (ZNF225); AT225   X52541; M62829       tristetraproline (TTP); TIS11; ZFP36;       growth factor-inducible nuclear protein 475 (NUP475)   M92843       purine-rich single-stranded DNA-binding protein alpha (PURA)   M96684       transcription factor relB; I-rel   M83221       CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-3       (ACTIVATING FACTOR 3)   L19871       octamer-binding transcription factor 1 (oct-1; OTF1);       octamer binding protein NF-A1; POU2F1   X13403       B-cell lymphoma 3-encoded protein (bcl-3)   M31732       retinoic acid receptor gamma 1 (RAR-gamma 1; RARG)   M24857; M38258;           M57707; M32074       PRB-binding protein E2F1; retinoblastoma-binding protein 3 (RBBP3);       retinoblastoma-associated protein 1 (RBAP1); PBR3   M96577       retinoic acid receptor alpha; retinoid X receptor alpha (RXRA)   X52773       major histocompatibility complex enhancer-binding protein MAD3   M69043       fuse-binding protein 2 (FBP2)   U69126       methyl CpG-binding protein 2 (MECP2)   L37298       AP4 basic helix-loop-helix DNA-binding protein   S73885       hepatocyte nuclear factor 4 (HNF4); transcription factor 14   X76930       metal-regulatory transcription factor   X78710       cockayne syndrome group A; WD-repeat protein (CSA protein)   U28413       RNase L inhibitor   X76388       40S ribosomal protein S5   U14970       glutamic-pyruvate transaminase 1 (GPT1);   D10355       alanine aminotransferase 1 (AAT1)       peptidylprolyl cis-trans isomerase A (PPIase; PPIA);       rotamase; cyclophilin A (CYPA);       cyclosporin A-binding protein   Y00052       probable protein disulfide isomerase ER-60 precursor       (ERP60); 58-kDa microsomal protein;       phospholipase C alpha   D16234; Z49835;           D83485; U42068       HSC70-interacting protein; progesterone receptor-associated P48 protein   U28918       chaperonin-containing T-complex polypeptide 1 beta subunit       (CCT-beta; CCTB; CCT2; TCP1-beta); 99D8.1   AF026293       peroxisome assembly factor-2 (PAF-2);       peroxisomal-type ATPase 1; peroxin-6; PEX6;       PXAAA1   U56602       CELLULAR RETINOIC ACID BINDING PROTEIN   S74445       endothelin-converting enzyme 1   Z35307       matrix metalloproteinase 14 precursor (MMP14); MMP-X1;       membrane-type matrix metalloproteinase 1 (MT-       MMP1)   D26512; X83535       bleomycin hydrolase (BLM hydrolase)   X92106       proteasome activator HPA28 subunit beta   D45248       placental plasminogen activator inhibitor 2       (PAI-2; PLANH2); monocyte ARG-serpin;       urokinase inhibitor   M18082; J02685       alpha-2-macroglobulin precursor (alpha-2-M)   M11313       tissue inhibitor of metalloproteinase 1 precursor (TIMP1);       erythroid potentiating activity (EPA); fibroblast collagenase inhibitor   X03124       alpha-1-antichymotrypsin precursor (ACT)   K01500       alpha-1-antitrypsin precursor; alpha-1 protease inhibitor; alpha-1-antiproteinase   X02920       DNA-binding protein A (DBPA); cold shock domain protein A (CSDA)   M24069       decoy receptor 3 (DCR3)   AF104419       T-complex protein 1 zeta-like subunit (CCT-zeta-like; TCP1-zeta-like); TSA303;       testis-specific TCP20#   D78333       chromatin assembly factor 1 p48 subunit (CAF1 p48 subunit);       retinoblastoma-binding protein 4 (RBBP4); RBAP48; msil protein homolog   X74262       high mobility group protein HMG2   X62534       DNA-binding protein UEV-1; UBE2V   U49278       activator 1 140-kDa subunit (A1 140-kDa subunit);       replication factor C large subunit;       DNA-binding protein PO-GA   L14922       replication factor C 36-kDa subunit (RFC36); activator 1 36-kDa subunit   L07540       replication factor C 38-kDa subunit (RFC38); activator 1 38-kDa subunit   L07541       replication protein A 70-kDa subunit (RPA70; REPA1; RF-A);       single-stranded DNA-binding protein   M63488       activator 1 40-kDa subunit (A1 40-kDa subunit);       replication factor C 40-kDa subunit (RFC40); RFC2   M87338       activator 1 37-kDa subunit; replication factor C 37-kDa subunit (RFC37); RFC4   M87339       DNA topoisomerase 1 (TOP1)   J03250       DNA topoisomerase II alpha (TOP2A)   J04088       proliferating cyclic nuclear antigen (PCNA); cyclin   M15796;           J04718       DNA topoisomerase II beta (TOP2B)   X68060       replication protein A 14-kDa subunit (RP-A) (RF-A); replication factor A protein 3   L07493       DNA nucleotidylexotransferase; terminal addition enzyme;       terminal deoxynucleotidyltransferase (TDT); terminal transferase; DNTT   M11722; K01919       DNA polymerase delta catalytic subunit   M80397       DNA topoisomerase III (TOP3)   U43431       excision repair cross-complementing rodent repair deficiency       complementation group 6 (ERCC6);       Cockayne syndrome protein 2 type B (CSB)   L04791       xeroderma pigmentosum group G complementing protein (XPG); X-ray repair-       complementing defective repair in Chinese hamster cells 5 (XRCC5)   L20046; X69978       Ku (p70/p80) subunit; ATP-dependent DNA helicase II 86-kDa subunit;       lupus ku autoantigen protein; thyroid-lupus autoantigen (TLAA);       CTC box binding factor 85-kDa subunit (CTCBF; CTC85); nuclear factor IV   M30938       xeroderma pigmentosum group B complementing protein (XPB);       excision repair cross-complementing rodent       repair deficiency complementation group 3 (ERCC3);       basal transcription factor 2 89-kDa subunit (BTF2-p89; TFIIH 89-kDa subunit)   M31899       Ku 70-kDa subunit; ATP-dependent DNA helicase II 70-kDa subunit;       lupus ku autoantigen protein P70; thyroid-lupus auto-antigen (TLAA);       CTC box binding factor 75-kDa subunit (CTC75)   M32865; S38729       X-ray repair-complementing defective repair in Chinese hamster cells 1 (XRCC1)   M36089       ubiquitin-conjugating enzyme E2 17-kDa (UBE2A); ubiquitin-protein ligase;       ubiquitin carrier protein; HR6A   M74524       DNA polymerase alpha catalytic subunit (POLA)   X06745       6-O-methylguanine-DNA methyltransferase (MGMT); methylated-DNA-protein-       cysteine methyltransferase   M29971       xeroderma pigmentosum group D complementing protein (XPD); X-ray repair-       complementing defective repair in Chinese hamster cells 2 (XRCC2)   X52221       excision repair cross-complementing rodent repair deficiency       complementation group 1 (ERCC1)   M13194       mutL protein homolog1 (MLH1); colon cancer nonpolyposis type 2 protein (COCA2)   U07418       UV excision repair protein RAD23 homolog B (HHR23B);       xeroderma pigmentosum group C repair complementing complex 58-kDa protein   D21090       HHR23A; UV excision repair protein protein RAD23A   D21235       DNA-dependent protein kinase (DNA-PK) +       DNA-PK catalytic subunit (DNA-PKCS)   U35835 + U47077       DNA damage repair &amp; recombination protein 52 (RAD52)   U12134       ataxia telangiectasia (ATM)   U33841       RAD50   U63139       DNA ligase IV (LIG4); polydeoxyribonucleotide synthase   X83441       DNA ligase III (LIG3); polydeoxyribonucleotide synthase   X84740       DNA mismatch repair protein MSH2   U04045; L47583       DNA mismatch repair protein MSH6; mutS alpha 160-kDa subunit;       G/T mismatch binding protein (GTMBP; GTBP)   U54777       RecQ protein-like (DNA helicase Q1-like)   D37984       DNA polymerase beta subunit (DPOB)   D29013       DNA mismatch repair protein PMS1 (PMS1 protein homolog 1)   U13695       DNA mismatch repair protein PMS2 (PMS1 protein homolog 2)   U13696       ATP-dependent DNA ligase I (LIG1); polydeoxyribonucleotide synthase   M36067       xeroderma pigmentosum group A complementing protein (XPA)   D14533       damage-specific DNA binding protein p48 subunit (DDBB P48); implicated in xeroderma       pigmentosum group E (DDB2)   U18300       DNA repair protein XRCC4   U40622       G/T mismatch-specific thymine DNA glycosylase (TDG)   U51166       DNA repair protein XRCC9   U70310       endonuclease III homolog 1; HNTH1; OCTS3   U79718       DNA-repair protein complementing XP-C cells; xeroderma pigmentosum group C       complementing protein (p125)   D21089       uracil-DNA glycosylase precursor (UNG1)   X15653       DNA-(apurinic or apyrimidinic site) lyase; AP endonuclease 1 (APE1);       apurinic/apyrimidinic endonuclease (APEX); APEX nuclease (APEN);       REF1   X59764; X66133       DNA repair protein RAD54 homolog   X97795       recA-like protein HsRad51; DNA repair protein RAD51 homolog   D13804       V(D)J recombination activating protein 2 (RAG2)   M94633       V(D)J recombination activating protein 1 (RAG1)   M29474       muscle-specific DNase I-like precursor (DNase1L1; DNL1L); DNase X   X90392; L40817; U06846       deoxyribonuclease I (DNase I)   M55983       dual-specificity protein phosphatase 9;       mitogen-activated protein kinase phosphatase 4       (MAP kinase phosphatase 4 (MKP4)   Y08302       G1/S-specific cyclin D3 (CCND3)   M92287       G1/S-specific cyclin D1 (CCND1); cyclin parathyroid adenomatosis 1 (PRAD1);       bcl-1 oncogene   X59798       G1/S-specific cyclin D2 (CCND2) + KIAK0002   M90813 + D13639       G2/mitotic-specific cyclin B1 (CCNB1)   M25753       G1/S-specific cyclin E (CCNE)   M73812       G2/mitotic-specific cyclin G1 (CCNG1; CYCG1)   U47413       G1/S-specific cyclin C   M74091       cyclin K   AF060515       protein serine/threonine kinase STK1; cell division protein kinase 7 (CDK7);       CDK-activating kinase (CAK); 39-kDa protein kinase   L20320       cyclin-dependent protein kinase 2 (CDK2); p33 protein kinase   M68520       extracellular signal-regulated kinase 2 (ERK2);       mitogen-activated protein kinase 2 (MAP kinase 2; MAPK 2); p42-MAPK   M84489       mitogen-activated protein kinase 3 (MAPK3; PRKM3); MAPK1;       extracellular signal-regulated kinase 1 (ERK1);       microtubule-associated protein 2 kinase; insulin-stimulated MAP2 kinase   X60188       extracellular signal-regulated kinase 3 (ERK3); MAP kinase 3 (MAPK3; p97-MAPK);       PRKM5   X80692       CDC-like kinase 3 (CLK3)   L29220       cell division protein kinase 4; cyclin-dependent kinase 4 (CDK4); PSK-J3   M14505       extracellular signal-regulated kinase 5 (ERK5); BMK1 kinase   U25278       cell division control protein 2 homolog (CDC2); p34 protein kinase;       cyclin-dependent kinase 1 (CDK1)   X05360       extracellular signal-regulated kinase 4 (ERK4); MAP kinase 4 (MAPK4; p63-MAPK);       PRKM4   X59727       cell division protein kinase 5 (CDK5); tau protein kinase II catalytic subunit       (TPKII catalytic subunit); serine/threonine protein kinase PSSALRE   X66364       extracellular signal-regulated kinase 6 (ERK6); stress-activated protein kinase-3;       mitogen-activated protein kinase p38 gamma; (MAP kinase p38 gamma)   X79483       serine/threonine-protein kinase PLK1 (STPK13)   U01038       checkpoint kinase 1 (CHK1)   AF016582       aurora- &amp; IPL1-like midbody-associated protein       kinase 1 (AIM1); ARK2   AF008552       cyclin G-associated kinase (GAK)   D88435       special AT-rich sequence binding protein 1   M97287       (SATB1); MAR/SAR DNA-binding protein       cyclin-dependent kinase inhibitor 1A (CDKN1A);       melanoma differentiation-associated protein 6 (MDA6);       CDK-interacting protein 1 (CIP1); WAF1; SDI1   U09579; L25610       wee1Hu CDK tyrosine 15-kinase; wee-1-like protein kinase   U10564       cyclin-dependent kinase 4 inhibitor 2B (CDKN2B); p14-INK4B;       multiple tumor suppressor 2 (MTS2)   U17075; L36844       helix-loop-helix protein HLH 1R21; DNA-binding protein inhibitor Id-3; HEIR-1   X69111       DNA-binding protein inhibitor ID-1; Id-1H   D13889       prothymosin alpha (PROT-alpha; PTMA)   M26708       40S ribosomal protein S19 (RPS19)   M81757       p55CDC   U05340       cell division cycle protein 25A (CDC25A); M-phase inducer phosphatase 1   M81933       CDC25B; CDC25HU2; M-phase inducer phosphatase 2   M81934; S78187       CDC25C; M-phase inducer phosphatase 3   M34065       growth inhibitory factor (GIF); metallothionein-III (MT-III; MT3)   D13365;           M93311       CDC37 homolog   U63131       cell cycle protein P38-2G4 homolog; HG4-1   U59435       btg protein precursor; NGF-inducible anti-proliferative protein PC3   U72649       RCL growth-related c-myc-responsive gene   AF040105       40-kDa heat-shock protein 1 (HSP40); DNAJ protein homolog 1 (HDJ1; DNAJ1)   D49547       60-kDa heat shock protein (HSP60); HSPD1; 60-kDa chaperonin;       mitochondrial matrix protein P1 precursor; p60 lymphocyte protein;       HUCHA60; GROEL   M34664       90-kDa heat-shock protein A (HSP90A); HSP86; HSPCA   X07270       27-kDa heat-shock protein (HSP27); stress-responsive protein 27 (SRP27);       estrogen-regulated 24-kDa protein; HSPB1   X54079       70-kDa heat shock protein 1 (HSP70.1; HSPA1)   M11717       heat shock 70-kDa protein 6 (heat shock 70-kDa protein B)   X51757; M11236       heat shock cognate 71-kDa protein; heat shock 70-kDa protein 8 (HSPA8; HSC70;       HSP73   Y00371       heat shock-related 70-kDa protein 2   L26336       major vault protein (MVP); lung resistance-related protein (LRP)   X79882       thiosulfate sulfurtransferase; rhodanese   D87292       soluble epoxide hydrolase (SEH); epoxide hydratase; cytosolic epoxide hydrolase (CEH);       EPHX2   L05779       serum paraoxonase/arylesterase 1 (PON1); serum aryldiakylphosphatase 1;       aromatic esterase 1 (A-esterase 1)   M63012       polymorphic arylamine N-acetyltransferase (PNAT) + monomorphic (MNAT)   X14672; X17059       quinone oxidoreductase; NADPH: quinone reductase; zeta-crystallin (CRYZ)   L13278; S58039       cytosolic superoxide dismutase 1 (SOD1)   K00065; X02317       cytochrome P450 IB1 (CYP1B1)   U03688       cytochrome P450 IIA6 (CYP2A6) + CYP2A7 + CYP2A13 +   M33318; M33316       CYP2A7PT + CYP2A7PC +       U22029 + U22030 + U22044       cytochrome P450 IIB6 (CYP2B6) + CYP2B3   M29874; J02864       cytochrome P450 IIIA3 (CYP3A3) + CYP3A4 + CYP3A5 + CYP3A7       M13785 + M18907 + J04813 + D00408       cytochrome P450 IVA11 (CYP4A11)   L04751       cytochrome P450 VIIA1 (CYP7A1)   X56088       D-amino acid oxidase (DAMOX; DAO; DAAO)   X13227       S-mephenytoin 4 hydroxylase; cytochrome P450 IIC9 (CYP2C9) + CYP2C10 +       CYP2C17 + CYP2C18 + CYP2C19   M21940 + M15331;           M21939 + M61858 +           M61854       cytochrome P450 IIE1 (CYP2E1)   J02625       cytochrome P450 IIF1 (CYP2F1)   J02906       cytochrome P450 IVB1 (EC 1.14.14.1) (P450-HP)   J02871       cytochrome P450 IA2 (P450-P3) (P450-4)   Z00036       plasma glutathione peroxidase precursor (GPXP; GPX3)   D00632; X58295       natural killer cell enhancing factor (NKEFB) + thiol-specific antioxidant protein       (TSA); thioredoxin peroxidase 1 (TDPX1);       thioredoxin-dependent peroxide reductase 1   L19185 + Z22548;           X82321       thioredoxin peroxidase 2 (TDPX2); thioredoxin-dependent peroxide reductase 2;       proliferation-associated gene (PAG);       natural killer cell enhancing factor A (NKEFA)   X67951       glutathione reductase (GRase; GSR; GR)   X15722       microsomal glutathione S-transferase 12 (GST12; MGST1)   J03746; B28083       glutathione S-transferase pi (GSTP1; GST3)   X08058; M24485       glutathione peroxidase (GSHPX1; GPX1)   Y00483; M21304       glutathione S-transferase theta 1 (GSTT1)   X79389       methallothionein IH (MT1H); metallothinein0       (MT0) + MT1I; MT2 + MT1L + MT1R   X64177 + X97260 +           X76717 + X97261       glutathione peroxidase-gastrointestinal (GSHPX-GI);       glutathione peroxidase-related protein 2 (GPRP)   X53463       heme oxygenase 1 (HO1); HSOXYGR   X06985       heme oxygenase 2 (HO2)   D21243; S34389       dimethylaniline monooxygenase (N-oxide forming) 1 (EC 1.14.13.8);       fetal hepatic flavin-containing monooxygenase 1 (FMO 1);       dimethylaniline oxidase 1   M64082       glutathione S-transferase mu1 (GSTM1; GST1); HB subunit 4; GTH4   X68676; S01719       glutathione S-transferase A1 (GTH1; GSTA1); HA subunit 1; GST-epsilon   M25627       glutathione-S-transferase (GST) homolog   U90313       glutathione synthetase (GSH synthetase; GSH-S); glutathione synthase   U34683       NAD(P)H dehydrogenase; quinone reductase; DT-diaphorase;       azoreductase; phylloquinone reductase; menadione reductase   J03934       growth arrest &amp; DNA-damage-inducible protein (GADD45);       DNA-damage-inducible transcript 1 (DDIT1)   M60974       tumor necrosis factor alpha precursor (TNF-alpha; TNFA); cachectin   X01394       lymphotoxin-alpha precursor (LT-alpha); tumor necrosis factor-beta (TNF-beta; TNFB)   D12614       fas antigen ligand (FASL); apoptosis antigen ligand (APTL; APT1LG1);       TNFSF6   D38122;       U08137       tumor necrosis factor receptor (TNFR) + tumor necrosis factor receptor 2 (TNFR2);       tumor necrosis factor binding protein 2 (TBP2)   M32315 + M55994       tumor necrosis factor receptor 1 (TNFR1); tumor necrosis factor binding protein 1       (TBP1); CD120A antigen   M33294       fasL receptor; apoptosis-mediating surface antigen fas; APO-1 antigen; CD95 antigen   M67454       retinoic acid receptor beta (RXR-beta; RXRB)   M84820; X63522; S54072       tumor necrosis factor receptor 1-associated death domain protein       (TNFR1-associated death domain protein; TRADD)   L41690       CD27BP (Siva)   U82938       tumor necrosis factor type 1 receptor associated protein (TRAP1)   U12595       caspase-2 precursor (CASP2); ICH-1L protease + ICH-1S protease   U13021 + U13022       interleukin-1 beta convertase precursor (IL-1BC); IL-1 beta converting enzyme (ICE);       p45; caspase-1 (CASP1)   U13699; M87507; X65019       caspase-6 precursor (CASP6); cysteine protease MCH2 isoforms alpha + beta   U20536 + U20537       caspase-4 precursor (CASP4); ICH-2 protease; TX protease;       ICE(REL)-II + caspase-5 precursor (CASP5); ICH-3 protease; TY protease;       ICE(REL)-III   U28014 + U28015       caspase-7 precursor (CASP7); ICE-like apoptotic protease 3 (ICE-LAP3);       apoptotic protease MCH-3; CMH-1   U37448       TNF-related apoptosis inducing ligand (TRAIL); APO-2 ligand (APO2L)   U57059       caspase-8 precursor (CASP8); ICE-like apoptotic protease 5 (ICE-LAP5);       MORT1-associated CED-3 homolog (MACH);       FADD-homologous ICE/CED-3-like protease (FADD-like ICE; FLICE);       apoptotic cysteine protease MCH-5   U60520; U58143;           X98172; AF00962       apoptosis regulator bax   L22474       apoptosis regulator bcl-x   Z23115; L20121; L20122       apoptosis regulator bcl-2   M14745       NIP3 (NIP3)   U15174       bcl2 homologous antagonist/killer (BAK)   U23765; U16811; X84213       induced myeloid leukemia cell differentiation protein MCL-1   L08246       BAD protein; bcl-2 binding component 6 (BBC6); bcl-2L8   U66879       BCL-2 binding athanogene-1 (BAG-1);       glucocorticoid receptor-associated protein RAP46   S83171; Z35491       interferon-inducible RNA-dependent protein kinase (P68 kinase)   M35663; U50648       inducible nitric oxide synthase (INOS); type II NOS; hepatocyte NOS (HEP-NOS)   L09210       defender against cell death 1 (DAD1)   D15057       clusterin precursor (CLU); complement-associated protein SP-40;       complement lysis inhibitor (CLI); apolipoprotein J (APOJ);       testosterone-repressed prostate message 2 (TRPM2);       sulfated glycoprotein 2 (SGP2)   M74816       growth arrest &amp; DNA-damage-inducible protein 153 (GADD153);       DNA-damage-inducible transcript 3 (DDIT3);       C/EBP homologous protein (CHOP)   S40706; S62138       inhibitor of apoptosis protein1 (HIAP1; API1) + IAP homolog C;       TNFR2-TRAF signaling complex protein 1; MIHC   U45878 + U37546       cytoplasmic dynein light chain 1 (HDLC1);       protein inihibitor of neuronal nitric oxide synthase (PIN)   U32944       apoptosis inhibitor survivin   U75285       sentrin; ubiquitin-like protein SMT3C;       ubiquitin-homology domain protein PIC1;       UBL1; SUMO-1; GAP modifying protein 1; GMP1   U83117       IEX-1L anti-death protein; PRG-1; DIF-2   AF039067; AF071596       poly(ADP-ribose) polymerase (PARP; PPOL); ADPRT;       NAD + ADP-ribosyltransferase; poly(ADP-ribose) synthetase   M18112; J03473       avian myelocytomatosis viral oncogene homolog (MYC)   V00568       p53-associated mdm2 protein   Z12020; M92424       platelet-derived growth factor B subunit precursor (PDGFB; PDGF2);       bacaplermin; c-sis   X02811; X02744;           M12783; M16288       p53 cellular tumor antigen   M14694;       M14695       MYB-related protein B (B-MYB); avian myeloblastosis viral       oncogene homolog-like 2 (MYBL2)   X13293       triiodothyronine receptor; thyroid hormone receptor (THRA1);       v-erbA-related protein ear-1   M24898       jun proto-oncogene; avian sarcoma virus 17 oncogene homolog;       transcription factor AP-1   J04111       insulin-like growth factor binding protein 2 (IGFBP2)   M35410       c-myc purine-binding transcription factor puf; nucleoside diphosphate kinase B       (NDP kinase B; NDKB) + nm23-H2S   L16785 + M36981       Abelson murine leukemia viral oncogene homolog 1 (ABL1)   M14752       retinoblastoma-associated protein (RB1); PP110; P105-RB   M15400       L-myc proto-oncogene (MYCL1)   M19720       breast cancer type 2 susceptibility protein (BRCA2)   U43746       fos-related antigen (FRA1); fosL1   X16707       nucleolar phosphoprotein B23; nucleophosmin (NPM); numatrin   M23613       c-myc binding protein MM-1   D89667       c-fos proto-oncogene; G0S7 protein   K00650       met proto-oncogene; hepatocyte growth factor   J02958       receptor precursor (HGF-SF receptor)       nucleoside diphosphate kinase A (NDKA); NDP kinase A;       tumor metastatic process-associated protein;       metastasis inhibition factor NM23 (NM23-H1)   X17620       matrix metalloproteinase 11 (MMP11); stromelysin 3   X57766       box-dependent myc-interacting protein 1   U68485       H-ras proto-oncogene; transforming G protein   V00574       protein-tyrosine phosphatase PTEN;       mutated in multiple advanced cancers 1 (MMAC1);       TEP1   U92436       prostaglandin G/H synthase 2 precursor (PGH synthase 2; PGHS2; PTGS2);       cyclooxygenase 2 (COX2); prostaglandin-endoperoxide synthase 2   M90100       78-kDa glucose regulated protein precursor (GRP 78);       immunoglobulin heavy chain binding protein (BIP)   M19645       complement 3 (C3)   K02765       interleukin-10 precursor (IL-10); cytokine synthesis inhibitory factor (CSIF)   M57627       thioredoxin (TRDX; TXN); ATL-derived factor (ADF);       surface-associated sulphydrylprotein (SASP)   J04026       enolase 1 alpha (ENO1); non-neural enolase (NNE);    M14328       phosphopyruvate hydratase (PPH)       biliverdin reductase A precursor (BLVRA; BVR)   U34877       tyrosine aminotransferase (TAT); I-tyrosine: 2-oxoglutarateaminotransferase   X52520       muscle-specific carbonic anhydrase III (CA3); carbonate dehydratase III   M29458       spermidine/spermine N1-acetyltransferase (SSAT);       diamine acetyltransferase; putrescine acetyltransferase   M55580       L-lactate dehydrogenase H subunit (LDHB)   Y00711       phosphoglyceride kinase 1 (PGK1; PGKA); primer recognition protein 2 (PRP2)   V00572       glucose-6-phosphate dehydrogenase (G6PD)   X03674       mitochondrial phosphoenolpyruvate carboxykinase 2 precursor (PEPCK-M; PCK2);       phosphoenolpyruvate carboxylase   X92720       galactoside 2-1-fucosyltransferase 2;       GDP-1-fucose: beta-D-galactoside 2-alpha-1-fucosyltransferase 2;       fucosyltransferase 2 (FUT2); secretor blood group alpha-2-fucosyltransferase;       secretor factor 2 (SE2)   D87942       galactosyltransferase-associated protein kinase p58 (GTA);       cell division cycle 2-like 1 (CDC2L1; CLK1)   M37712       adrenodoxin   M34788       alcohol dehydrogenase alpha subunit + alcohol       dehydrogenase 2 + alcohol       dehydrogenase 3   M12271 + D00137 + X04299       alcohol dehydrogenase 5 chi polypeptide   M30471       alcohol dehydrogenase class II pi subunit   M15943       CREATINE KINASE B CHAIN   L47647       fatty acid synthase   S80437       hepatic triglyceride lipase (HTGL)   X07228       bile-salt-activated lipase   M85201; M37044       mitochondrial enoyl-CoA hydratase short subunit 1   D13900       peroxisomal bifunctonal enzyme   L07077       peroxisomal acyl-CoA oxidase branched subunit (BRCOX)   X95190       acyl-CoA dehydrogenase long chain-specific precursor (LCAD; ACADL)   M74096       alcohol sulfotransferase   L20000       estradiol 17 beta-dehydrogenase 1   M36263       cytochrome P450 XVIIA1 (CYP17A1)   M14564       peroxisomal 3-ketoacyl-CoA thiolase precursor (PTHIO);       peroxisomal 3-oxoacyl-CoA thiolase; beta-ketothiolase;       acetyl-CoA acyltransferase (ACAA)   X14813       3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMG-CoA reductase; HMGCR)   M11058       lipoprotein lipase precursor (LPL)   M15856       lung group IB phospholipase A2 precursor (PLA2);       phosphatidylcholine 2-acylhydrolase   M21054       mitochondrial cytochrome P450 XIA1 precursor; P450(SCC);       cholesterol side-chain cleavage enzyme; cholesterol desmolase CYP11A1   M14565       dihydrofolate reductase (DHFR)   V00507       thymidylate synthase (TYMS; TS)   X02308       cytosolic thymidine kinase (TK1)   K02581       ribonucleoside-diphosphate reductase M1 subunit; ribonucleotide reductase   X59543       microsomal UDP-glucuronosyltransferase 2B15 precursor (UDPGT); UDPGTH-3;       UGT2B15 + microsomal 2B10 precursor (UDPGT); UGT2B10 + 2microsomal       B8 precursor   U08854; X63359;           U06641; J05428;           Y00317       GLCLC, GLCL (Glutamate-cysteine ligase catalytic subunit,       gamma-glutamylcysteine synthetase)   M90656       gamma-glutamyl hydrolase precursor (GGH; GH);       folylpolygammaglutamyl hydrolase;       gamma-glu-X carboxypeptidase; conjugase   U55206       3′-phosphoadenosine 5′-phosphosulfate       synthase 1 (PAPS synthase 1; PAPSS1);       PAPS synthetase 1; sulfurylase kinase 1 (SK1)   Y10387       soluble glutamic oxaloacetic transaminase 1 (GOT1);       cytoplasmic aspartate aminotransferase 1; transaminase A   M37400       alcohol dehydrogenase 6 + aldehyde dehydrogenase 1 (ALDH1)   K03000       peroxisomal acyl-coenzyme A oxidase   S69189       very-long-chain-specific acyl-CoA dehydrogenase precursor (VLCAD)   D43682       glutamate-cysteine ligase regulatory subunit (GLCLR);       gamma-glutamylcysteine synthetase   P48507       LOX (Protein-lysine 6-oxidase, Lysyl-Oxidase)   M94054       ornithine decarboxylase   X16277       corticosteroid 11-beta-dehydrogenase isozyme 2   U14631       cytochrome P450 VA1 (CYP5A1)   M80647       mitochondrial aldehyde dehydrogenase precursor (class 2); ALDHI; ALDH2   Y00109       5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (DHICA oxidase);       tyrosinase-related protein 1 (TRP-1); catalase B; glycoprotein-75 (GP75)   X51420       tenascin precursor (TN); hexabrachion (HXB); cytotactin; neuronectin; GMEM;       miotendinous antigen; glioma-associated extracellular matrix antigen   X78565; M55618       OSTEOPONTIN PRECURSOR (BONE SIALOPROTEIN 1)   X13694       ATP-binding cassette transporter (ABCR)   U88667       tissue inhibitor of metalloproteinase 2 precursor (TIMP2)   J05593       matrix metalloproteinase 15 (MMP15)   Z48482       matrix metalloproteinase 14 (MMP14)   D26512       matrix metalloproteinase 1 (MMP1)   X54925       vinculin   M33308       vimentin (VIM)   X56134; M14144       serum amyloid A1 precursor (SAA1)   M23698       senescence marker protein 30 (SMP30); regucalcin (RGN; RC)   D31815       ubiquitin cross-reactive protein precursor (UCRP);       alpha-inducible interferon; interferon-induced 17-kDa protein; G1P2; ISG15   M13755       laminin gamma 2 subunit precursor (LAMC2)   Z15009       peroxisome assembly factor 1 (PAF1);       peroxisomal membrane protein 3 (PXMP3; PMP3);       35-kDa peroxisomal membrane protein (PMP35); peroxin 2 (PEX2)   M86852       peroxisomal membrane protein 69 (PMP69)   AF009746       peroxisome biogenesis disorder protein 1 (PEX1)   AF026086       mitochondrial glutamic oxaloacetic transaminase 2 (GOT2);       aspartate aminotransferase 2; transaminase A   M22632       nck, ash &amp; phoshpholipase C gamma-binding protein (NAP4)   AB005216       N-oxide-forming dimethylaniline monooxygenase 4;       hepatic flavin-containing monooxygenase 4 (FMO4)   Z11737       xeroderma pigmentosum group F complementing protein (XPF);       DNA excision repair protein ERCC4; ERCC11   L77890       replication protein A 30-kDa subunit; replication factor A protein 4 (RPA4; RFA)   U24186       mutY homolog (hMYH)   U63329       beta crystallin A4 (CRYBA4)   U59057       T-complex protein 1 epsilon subunit (TCP1-epsilon); CCT-epsilon (CCTE; CCT5)   D43950       beta crystallin B1 (CRYBB1)   U35340       beta crystallin B2 (CRYBB2); BP   L10035       beta crystallin B3 (CRYBB3; CRYB3)   U71216       mitochondrial 10-kDa heat shock protein (HSP10);       10-kDa chaperonin (CPN10); HSPE1   U07550       heat shock protein beta 3 (HSPB3); heat shock 17-kDa protein; HSPL27   U15590       probable protein disulfide isomerase P5 precursor   D49489       90-kDa heat-shock protein beta (HSP90); 84-kDa heat-shock protein beta (HSP84);       HSPCB   M16660       microsomal UDP-glucuronosyltransferase 1-6 precursor       (UDPGT; UGT1.6; UGT1F; GNT1)   J04093       glutathione S-transferase mu 3 (GSTM3); GST5   J05459       cytochrome P450 1A1 (CYP1A1); P450-P1; P450 form 6; P450-C   K03191       peroxisome proliferator activated receptor alpha (PPAR-alpha; PPARA)   L02932       protein disulfide isomerase-related protein precursor (PDIR)   D49490       liver carboxylesterase precursor; acyl coenzyme A: cholesterol acyltransferase (ACAT);       monocyte/macrophage serine esterase (hMSE); CES2   L07765       serum paraoxonase/arylesterase 3 (PON3); serum aryldiakylphosphatase 3;       aromatic esterase 3 (A-esterase 3)   L48516       cytochrome P450 XXIB (CYP21B); steroid 21-hydroxylase; CYP21A2   M12792; M23280       cytochrome P450 IID6 (CYP2D6); P450-DB1; debrisoquine 4-hydroxylase   M20403       microsomal UDP-glucuronosyltransferase 1-1 precursor       (UDPGT; UGT1.1; UGT1A; GNT1); bilirubin-specific isozyme 1 (hUG-BR1)   M57899       microsomal UDP-glucuronosyltransferase 1-4 precursor       (UDPGT; UGT1.4; UGT1D; GNT1); bilirubin-specific isozyme 2 (hUG-BR2)   M57951       flavin-containing amine oxidase B (MAOB); monoamine oxidase   M69177       eukaryotic peptide chain release factor subunit 1 (ERF1); TB3-1; C11 protein   M75715       microsomal UDP-glucuronosyltransferase 1-3 precursor       (UDPGT; UGT1.3; UGT1C; GNT1)   M84127       structure-specific recognition protein 1 (SSRP1);       recombination signal sequence recognition protein; T160   M86737       microsomal UDP-glucuronosyltransferase 1-2 precursor       (UDPGT; UGT1.2; UGT1B; GNT1); HLUGP4   S55985       thiopurine S-methyltransferase (TPMT)   S62904       meiotic recombination protein DMC1/LIM15 homolog   D63882       short/branched chain-specific acyl-CoA dehydrogenase precursor (SBCAD; ACADSB);       2-methyl branched chain acyl-CoA dehydrogenase (2-MEBCAD)   U12778       cytochrome P450 XIB1 precursor (CYP11B1); steroid 11-beta-hydroxylase (S11BH)   X55764       cytochrome P450 IVA11 (CYP4A11)   X71480       NADH-cytochrome B5 reductase (B5R); DIA1   Y09501       coproporphyrinogen III oxidase precursor (CPO); coproporphyrinogenase;       coprogen oxidase (COX)   Z28409       110-kDa heat-shock protein (HSP110); 105-kDa heat-shock protein (HSP105);       KIAA0201   D86956       gamma crystallin C (CRYGC; CRYG3;       gamma crystallin 2 + gamma crystallin B (CRYGB; CRYG2);       gamma crystallin 1-2   U66582 + M11971; M11970       heat shock transcription factor 4 (HHSF4)   D87673       extracellular superoxide dismutase precursor (EC-SOD; SOD3)   J02947       DNAJ protein homolog 2 (DNAJ2; hDJ2; HSJ2)   D13388       DNA mismatch repair protein MSH3; divergent upstream protein (DUP);       mismatch repair protein 1 (MRP1)   J04810       protein disulfide isomerase-related protein ERP72 precursor   J05016       replication protein A 32-kDa subunit (RPA32);       replication factor A protein 2 (REPA2; RPA2; RFA)   J05249       multidrug resistance-associated protein 1 (MRP1)   L05628       calnexin precursor (CANX);       major histocompatibility complex class I       antigen-binding protein p88; IP90   L10284; L18887;           M94859; M98452       cyclophilin-40 (CYP40; CYPD); 40-kDa peptidyl-prolyl cis-trans isomerase (PPIASE);       rotamase; cyclophilin-related protein   L11667       heat shock 70-kDa protein 4 (HSPA4); HSP70RY;       heat shock 70-related protein APG-2   L12723       T-complex protein 1 theta subunit (TCP1-theta);       CCT-theta (CCTQ; CCT8); KIAA0002   D13627       mitochondrial stress-70 protein precursor; 75-kDa glucose-regulated protein (GRP75);       peptide-binding protein 74 (PBP74); mortalin (MOT); HSPA9B   L15189       p23; 23-kDa progesterone receptor-associated protein   L24804; L24805       FLAP endonuclease 1 (FEN1); maturation factor 1 (MF1)   L37374       FK506-binding protein 12 (FKBP12); peptidyl-prolyl cis-trans isomerase (PPIase);       rotamase   M34539; M80199;           M92423; X55741;           X52220       heat shock factor protein 2 (HSF2); heat shock transcription factor 2 (HSTF2)   M65217       3-methyladenine DNA glycosylase (ADPG); 3-alkyladenine DNA glycosylase;       N-methylpurine-DNA glycosirase (MPG)   M74905       calreticulin precursor (CRP55); calregulin; HACBP; ERP60;       52-kDa ribonucleoprotein autoantigen RO/SS-A   M84739       transformation-sensitive protein IEF SSP 3521   M86752       alpha crystallin B subunit (alpha(B)-crystallin; CRYAB; CRYA2);       Rosenthal fiber component   S45630       heat shock protein beta 2 (HSPB2); DMPK-binding protein; MKBP   S67070       alpha crystallin A chain (CRYAA; CRYA1)   U05569       nicotinamide N-methyltransferase (NNMT)   U08021       phenol-sulfating phenol sulfotransferase 1 (PPST1);       thermostable phenol sulfotransferase (TS-PST);       HAST1/HAST2; ST1A3; STP1 + PPST2; ST1A2;       STP2 + monoamine-sulfating phenol sulfotransferase   U09031 + U28170 +           L19956       NADP + dihydropyrimidine dehydrogenase precursor (DPD);       dihydrouracil dehydrogenase; dihydrothymine dehydrogenase (DPYD)   U09178       transcriptional regulator atrX; X-linked helicase II (XH2);       X-linked nuclear protein (XNP); RAD54L   U09820       26S proteasome regulatory subunit S2 (PSMD2);       tumor necrosis factor type 1 receptor-associated protein (TRAP2); 55.11 protein   U12596       damage-specific DNA-binding protein p127 subunit (DDBA p127); DDB1   U18299       T-complex protein 1 delta subunit (TCP1-delta); CCT-delta (CCTD; CCT4);       stimulator of tar RNA binding (SRB)   U38846       7,8-dihydro-8-oxoguanine triphosphatase (8-oxo-dGTPase); mutT homolog 1 (MTH1)   D16581       150-kDa oxygen-regulated protein ORP150   U65785       48-kDa FKBP-associated protein (FAP48)   U73704       T-complex protein 1 eta subunit (TCP1-eta); CCT-eta (CCTH; CCT7);       HIV-1 NEF interacting protein   U83843       catalase (CAT)   X04076       porphobilinogen deaminase (PBGD); hydroxymethylbilane synthase (HMBS);       pre-uroporphyrinogen synthase   X04808       Mn+ superoxide dismutase 2 precursor (SOD2)   X07834; X59445       94-kDa glucose-regulated protein (GRP94); endoplasmin precursor; GP96 homolog;       tumor rejection antigen 1 (TRA1)   X15187; M33716       uracil-DNA glycosylase 2 (UNG2)   X52486       T-complex protein 1 alpha subunit (TCP1-alpha); CCT-alpha (CCTA; CCT1)   X52882       40S ribosomal protein S3 (RPS3)   X55715       47-kDa heat shock protein precursor; collagen-binding protein 1 (CBP1);       colligin 1 + collagen binding protein 2 (CBP2)   X61598 + D83174       T-complex protein 1 gamma subunit (TCP1-gamma);       CCT-gamma (CCTG; CCT3); TRIC5   X74801; U17104       transcription factor IIH (TFIIH); 52-kDa basic transcription factor 2 subunit (BTF2p52)   Y07595       x-ray repair cross-complementing protein 2 (XRCC2)   Y08837       8-oxyguanine DNA glycosylase 1 (OGG1); mutM homolog (MMH)   Y11838       34-kDa basic transcription factor 2 subunit (BTF2p34)   Z30093       N-oxide forming dimethylaniline monooxygenase 5;       hepatic flavin-containing monooxygenase 5 (FMO5); dimethylaniline oxidase 5   L37080       ubiquitin-like protein NEDD8   D23662       multidrug resistance protein 3 (MDR3); P-glycoprotein 3 (PGY3)   M23234       ubiqitin-conjugating enzyme E2-17-kDa (UBE2B); ubiquitin-protein ligase;       ubiquitin carrier protein; HR6B   M74525       p59 protein; HSP-binding immunophilin (HBI);       possible peptidyl-prolyl cis-trans isomerase (PPIase);       rotamase; 52-kDa FK506-binding protein (FKBP52);       FKBP59; HSP56; FKBP4   M88279       heat shock protein 40 homolog (HSP40 homolog); DNAJW   U40992       51-kDa FK506-binding protein (FKBP51);       peptidyl-prolyl cis-trans isomerase (PPIase);       rotamase; 54-kDa progesterone receptor-associated immunophilin;       FKBP54; FF1 antigen; HSP90-binding immunophilin   U42031       hematopoietic progenitor kinase (HPK1)   U66464       SPS1/Ste20 homolog KHS1   U77129       liver glyceraldehyde 3-phosphate dehydrogenase (GAPDH; G3PDH)   X01677       brain-specific tubulin alpha 1 subunit (TUBA1)   K00558       HLA class I histocompatibility antigen C-4 alpha subunit (HLAC)   M11886       cytoplasmic beta-actin (ACTB)   X00351       23-kDa highly basic protein; 60S ribosomal protein L13A (RPL13A)   X56932       40S ribosomal protein S9   U14971       ubiquitin   M26880       phospholipase A2   M86400       hypoxanthine-guanine phosphoribosyltransferase (HPRT)   V00530                                  
 
       [0047] It is particularly preferred if the methylation state of essentially all of the genes listed in Table 1 is investigated.  
       [0048] A set of genes is preferably investigated for methylation in which up to 25% of the genes listed in Table 1 are not contained.  
       [0049] It is further preferred that at least 95% of the genes listed in Table 1 are investigated for their methylation state, together with a limited number of additional unlisted genes.  
       [0050] Up to 25% of the genes listed in Table 1 are replaced according to the invention by a complete set of other unlisted genes.  
       [0051] Preferably, the chemically pretreated DNA sequence of the genes to be detected coincides at least to 95% with the correspondingly pretreated DNA sequence of the genes from Table 1.  
       [0052] Sequences, which coincide 100% in a segment of the exon that is at least 25 base pairs long are designated homologous in this invention. This is true also for sequences whose homology is recognized only by taking into consideration possible frameshifts.  
       [0053] Several of the genes under investigation and their importance for toxicological processes are introduced in the following examples.  
       [0054] The genomic sequences of the genes under investigation can be derived by comparison of the respective cDNA sequences with publicly accessible databases, in which genomic sequences are deposited. 
     
    
    
     EXAMPLE 1  
     Culturing HT-29 P208 Cells, Harvesting Cells and Preparation of Chromosomal DNA  
     [0055] HT-29 P208 cells (5×10 4  cells/ml) were seeded in culture dishes (33×5 cm) and grown for 5 days in DMEM/Ham&#39;s F-12 medium, which was supplemented with 10% fetal calf serum at 37° C. and 5% CO 2 , up to 95% confluence (Campbell-Thompson, M. and Bhardwaj, B., Cancer Research 2001, 61, 632-640). The cells were then incubated for 24 h in medium not containing calf serum. After repeated change of medium, the cells were incubated in 3 parallel cultures for 6 h and 24 h, either with medium, medium supplemented with 10 ng/ml TGF-b1, medium supplemented with 10 ng/ml IL-1b, medium supplemented with trichostatin (50 nM) or medium supplemented with milrinone (50 μM). The cells freed of medium were treated with trypsin, centrifuged, and resuspended in 200 μl of PBS buffer (Fritsch and Maniatis eds., Molecular Cloning: A Laboratory Manual, 1989), and stored at −20° C. The chromosomal DNA was purified with a QIAamp Kit according to the manufacturer&#39;s instructions (Qiagen, Hilden).  
     EXAMPLE 2  
     Production of Bisulfite-Treated DNA and Conducting the PCR Reactions  
     [0056] The DNA samples (20 ng) were digested with the restriction enzyme Mss1. The digested DNA was chemically converted with hydrogen sulfite (bisulfite, disulfite) and a radical trap at elevated temperature (DE 10050942). In this way, after alkaline hydrolysis, all unmethylated cytosines are converted to uracil, which correspond in their base-pairing behavior to thymidine. In contrast, 5-methylcytosine is not modified under these conditions.  
     [0057] The chemically pretreated DNA was then amplified with the use of a heat-stable DNA polymerase in a polymerase chain reaction. The multiplex PCR reactions were conducted with a thermocycler (Eppendorf GmbH) with the use of 10 ng of bisulfite-treated DNA, each time with 6 μmol of primer oligonucleotides (mixture of up to 32 individual primer oligonucleotides; see Table 3), 800 μM dNTPs and 4.5 mM magnesium chloride. The cycler program was as follows: step 1, 14 min at 96° C.; step 2, 60 sec 96° C.; step 3, 45 sec 55° C.; step 4, 75 sec 72° C.; step 5, 10 min at 72° C.; steps 2 to 4 were repeated 39 times.  
     [0058] The DNA fragments of 64 different genes listed in Table 3 were amplified with 6 sets of multiplex PCR (mPCR) and with bisulfite-treated DNA as the template, as described above. The mPCR reactions (I, J, K, L, M, N) of the genomic, bisulfite-treated DNA were conducted with the combination of primer oligonucleotides as listed in Table 3. It is also possible, however, to use other primer oligonucleotides in the same way for the amplification of the genomic, bisulfite-treated DNA. The primer pairs listed in Table 1, however, are particularly preferred.  
     EXAMPLE 3  
     Determination of the Methylation State of Selected Genes  
     [0059] The amplificates produced in Example 2 were hybridized with 512 oligonucleotides, which were bound to a solid phase (Model, F. and Adorjian, P., Bioinformatics 2001, 17 Suppl. 1, 157-164). The solid phase loaded with oligonucleotides is named an oligonucleotide array below. The detectability of the hybridization product is based on primer oligonucleotides fluorescently labeled with Cy5, which were used for the amplification. A hybridization reaction of the amplified DNA with the oligonucleotide, for example, GTTTTTTTCGTTTTAGAG (Sequence ID 6), occurs only when a methylated cytosine is present at the said site of the bisulfite-treated DNA. Thus, the methylation state of the specific cytosine can be determined by means of the hybridization product. In order to verify the methylation state of said position, an oligonucleotide is found on the oligonucleotide array, which permits it to detect the unmethylated cytosine. This oligonucleotide is identical to the oligonucleotide which was previously used for the analysis of the methylated status of the sample, with the exception that the oligonucleotide bears a thymine base instead of a cytosine base at the position to be analyzed, e.g., GTTTTTTTTGTTTTAGAG (Sequence ID 7). Thus, a hybridization reaction occurs only if an unmethylated cytosine is present at the position to be analyzed.  
     [0060] The fluorescent signals are detected by scanning the oligonucleotide arrays with the fluorescence scanner Genpix 4000A (Axon Instruments, USA). The quantitative determination of the fluorescent signals is made with the analytical software Genepix 3.0 (Axon Instruments, USA).  
     [0061] In order to be able to assign methylation patterns to a specific treatment of the cells, the DNA methylation patterns of HT29-P208 cells grown with IL-1b (interleukin) or cells treated with TGF-b1 (transforming growth factor) were determined. The results obtained were stored in databases and CpG dinucleotides with different methylation states were identified. The methylation patterns were compared by cluster analyses and statististical methods (Model, F. and Adorjan, P., Bioinformatics 2001, 17 Suppl. 1, 157-164).  
     EXAMPLE 4  
     Change of the Methylation State in HT29 Cells Due to Exogenous Cytokines and Active Substances of Low Molecular Weight  
     [0062] In this Example, the PCR products (see Table 1) of a cell culture (see Example 1), were amplified with CyS-fluorescently labeled primers of bisulfite-treated DNA, mixed, and hybridized on glass slides on which a pair of immobilized oligonucleotides was placed at each position. Each of these detection oligonucleotides was designed to hybridize the bisulfite-converted sequences found at CpG sites, which had been present originally in either the unmethyled (TG) or methyled (CG) state. The hybridization conditions were selected so as to display the detection of differences of the TG and CG variants in the individual nucleotides. The ratios of the two signals were calculated on the basis of a comparison of the intensities of the fluorescing signals.  
     [0063] The information is subsequently defined in a weighted matrix (see FIGS. 1, 2) for the differences in CpG methylation between two classes of HT29-P208 cells: treated and untreated. The p-value for weighted methylation (p&lt;0.05, F. Model, P. Adorjan, A. Olek, C. Piepenbrock, Feature selection for DNA methylation based cancer classification. Bioinformatics. 2001 June; 17 Suppl 1:S157-64) shows a clear difference between the two groups, which can be recognized from the variable gray shading. A higher degree of methylation correlates with a darker gray value.  
     [0064] Comparative investigations of the methylation state of 64 gene fragments (see Table 1) of HT29-P208 cells showed that both IL-1b as well as also TGF-b1 lead to a change of the methylation state of specific genes. In contrast to the controls (HT29-P208 in medium), a smaller degree of methylation could be found by supplementing the medium with TGF-b1, while a greater degree of methylation of various CpG-positions could be found by supplementing the medium with IL-1b. The changes in the methylation state were visible after a treatment time of 24 h (see FIGS. 1 and 2). After 6 h of treatment time no significant differences in methylation could be detected (data not shown). With the exception of CpG positions of the TGF-a gene, TGF-b1 and IL-1b change the methylation state of different genes.  
     [0065]FIG. 3 shows quantitatively the methylation state of selected CpGs for the genes TGF-a, EGFR, ANT1 and E-cadherin. The amplification of these genes is performed under the conditions described in Example 2. Table 2 summarizes the primer sequences used, their Seq ID, the length of the PCR fragment, as well as the oligonucleotides used for the methylation analysis with their Seq ID. The methylation state was determined by the calculation of the quotient of the fluorescent signal of the CG oligos over the sum of the fluorescent signals of both the TG and CG oligos. Thus, the methylation state can vary between 0 and 1, whereby 0 indicates the minimum and 1 indicates the maximum methylation state. For the CpG positions investigated here, a significant reduction of the methylation state was determined in HT29-P208 cells due to the treatment with TGF-b1 (see FIG. 3). In contrast, treatment with IL-1b led to no change or to an increase in the methylation state (see FIG. 3, A1 and 2, B1 and 2, D1). In another experiment, the effect of milrinone and trichostatin on the methylation state of selected CpG positions of the genes EGFR, ANT1 and CDC25A was investigated. The treatment of HT29-P208 cells with milrinone led to a reduction in the methylation state, but an increase occurred with trichostatin (see FIG. 4).  
     EXAMPLE 5  
     Methylation Analysis of the Cyp1a1 Gene  
     [0066] Genes which code for enzymes that catalyze the biotransformation of toxicological substances are particularly preferred in the analysis of modified methylation patterns, which in turn reflect changes in gene expression. A central function has been imputed in this way, among others, to the genes of the cytochrome P450 family. Among other things, it could be shown in animal experiments that one of the genes of this class, Cyp1a1, was induced after mice were exposed to beta-naphthoflavone (Arch Biochem Biophys Apr. 1, 2000;376(1):66-73). First, the genomic DNA sequence that encodes the Cyp1a1 gene must be identified for the methylation analysis. For this purpose, for example, the cDNA sequence (Genbank Acc. No. 000499) will be compared with a genomic database (e.g. Genbank htgs) whereby usually the BLAST comparison algorithm, which is available via the Internet (www.ncbi.nlm.nih.gov), is used. Therefore, in the present case, the segment of genomic DNA, which codes for Cyp1a1, can be identified (Genbank Acc. AC020705). Preferably, genomic segments in the region of the promoter as well as of the first exon or intron are investigated for differences in methylation, since relevant CpG dinucleotides, whose methylation influences gene expression, can preferably be found in these segments. In the example of the Cyp1a1 gene, exon 1 (underscored) was localized in the following genomic sequence segment:  
     [0067] &gt;genomic region, which contains exon 1 of the Cyp1a1 gene (exon 1 in bold letters)  
                          &gt;genomic region, which contains exon 1 of the           Cyp1a1 gene (exon 1 in bold letters)       catgccaaatggcactggggcttcgtgtcgtgccacagcgtggaccgaaa               atgcggacacatgcaggctgcctctcctcgcaggcagaagccacacgcag               acctagaccctttgcaccgcatccccttattcaatcgcgcacccgccacc               cttcgacagttcctctccctccaccccaaccccacgccgcgcgcgaggct               ggccctttaagagccccgccccgactccctcccccctcgcgtgactgcga               gcccccgcgccgggccggggaatgggtcggctgggtggctgcgcgggcct               ccggtccttctcacgcaacgcctgggcaccgcgcctccgggccaggtggg               gcggggacgggccgcctgacctctgccccctagagggatgtcgccggcgc               acgcaagctagccgggggtagggtgggggctccgcgccaggtgccccctc               cgtggtccctgggcccgagtctttccgtggccccccgccgccggatttct               gtgctctgccaatcaaagcactagccaccccgggagccaagagggaccct               caagggccggtgggtcctggctggagggaccgcgcgttgcaatcagcact               aaggcgatcctagaggctgcgaggagccgctagtgagcgctcagcgagcc               tgccccttcgccatccattccgatccttcaatcaagaggcgcgaacctca               gctagtcgcccgggctctgggggacaggtccagccccgcggcgcctctgg               ccttccggcccccgtgacctcagggctggggtcgcagcgcttctcacgcg               agccgggactcagtaaccccgggaaggaggtcaccacggggcagccccgc               ccccgcctgccgagtcctggtaggctgtagcgctggggaggcatctgcac               gcccagcgttccagtgggtgcaaaaatgacgaagaggagtccccgcgccc               caggatggagcttcccgtaccctctcttcgggctgtcctgggacttctcc               ctcaagccccctcctcggctgggttctgcactgcccttgggacgccttgg               aattgggacttccaggtgttcccagccctcacccctctatgtacaggcac               cgagatgtgtcccatagtgggttcttgcccacccgaccccccacccccgc               cgccctccgccacctttctctccaatcccagagagaccagcccggttcag               gctgcttctccctccatctcagctcgctccagggaaggaggcgtggccac               acgtacaagcccgcctataaaggtgcagtacttcaccctcaccc tgaagg                   tgacagttcttggatgttccctgatccttgtgatcccaggctccaagagt                   ccacccttcccagctcagctcag tacctcaggtgagttgctgggggactt               ctggcttgccctttctctcccaataaaaggaacattttggtgcctccagg               acttcttaggtagctacctgtctagcacctccaaaaagggaggctcagag               tgtttttagtgaccaggcagtctagccccctagtggggaaactgaggcca               ggggaagaggaggacttgcccatggtcccacagctggtaccagacctcta               gatacagatggcatctcattcaggacttcaggacccaggctccagctcca               tcccctagtgagtgtctccctgcctaccctggggcttccccatcaaggcc               acctggcaggctggaatatgtgcagcccctccctcaggctttctgatgac               aggggcttctccttgggtggacagggtggatggagggggtgggctgggtt               cttaccagctgtaccctgccctagcctaagaagctacccctggcagattt               taccctcctaagggtggcttgtcagtgctgagatgtcctagacagctggg               acaatagaggcagatctgtgcaggagtcccaggcctttcctatctcattg               accatcttctttgtcctttgctgggagacaatcagggtgacagattgcca               actgcagggagctggaaataccagtccctaaaaactcaccagtcacatct               cccttggcctcctaccatcttacaaaggctccagctccatcccctagtga               gtgtctccctgcctaccctggggcttccccataaagccacctggcaggct               ggaatatgtgcagcccctccctcaggctttctgatgacagcccctccagg               aagcctcccctccactataatacttgtggtaggaaccatccatctccctg               tcttgtgaggttctcctgtggggagcctaactggtaagactgtcattccc               cacagcagatctgggttttctcttccctctggatccagctgggtactctg               aactgagagatcttgtcttaccctctctcagatgttgaaattggacccca               gaaaagtaaaatgtgcagtccaagatcactttgactagaatgttggtcta               ctgacctctagtccagggtaacaggcagagatgcctgatatgttggagag               agtggtttatgaatttaaacaccctttttaggtcaagcttacagagaaag               tattgcctcagtttcctttcagtttagatccattcctgatttccctgatt               ccagtctggggttttcttacagcctagtgggaaccttccatttattctct               gctctctggtaacctgcaaaagggggaggtccaaactgttcattcattga               gaa          
 
     [0068] Sequence segment after bisulfite treatment and PCR amplification (the primer oligonucleotides used and the analyzed CpG are given in bold letters)  
                          &gt;cyp1a1 sense-1 bisulfite             tatgttaaatggtattgg ggtttCGtgtCGtgttatagCGtggatCGaaa               atgCGgatatatgtaggttgttttttttCGtaggtagaagttataCGtag               atttagattttttgtatCGtatttttttatttaatCGCGtattCGttatt               tttCGatagtttttttttttttattttaattttaCGtCGCGCGCGaggtt               ggttttttaagagtttCGtttCGatttttttttttttCGCGtgattgCGa               gttttCGCGtCGggtCGgggaatgggtCGgttgggtggttgCGCGggttt               tCGgttttttttaCGtaaCGtttgggtatCGCGttttCGggttaggtggg               gCGgggaCGggtCGtttgatttttgttttTtagaGggatgtCGtCGgCGt               aCGtaagttagtCGggggtagggtgggggtttCGCGttaggtgttttttt               CGtggtttttgggttCGagttttttCGtggtttttCGtCGtCGgattttt               gtgttttgttaattaaagtattagttatttCGggagttaagagggatttt               taagggtCGgtgggttttggttggagggatCGCGCGttgtaattagtatt               aaggCGattttagaggttgCGaggagtCGttagtgagCGtttagCGagtt               tgttttttCGttatttatttCGattttttaattaagaggCGCGaatttta               gttagtCGttCGggttttgggggataggtttagtttCGCGgCGtttttgg               tttttCGgttttCGtgattttagggttggggtCGtagCGttttttaCGCG               agtCGggatttagtaatttCGggaaggaggt tattA CG GGg tagtttCGt               tttCGtttgtCGagttttggtaggttgtagCGttggggaggtatttgtaC               GtttagCGttttagtgggtgtaaaaatgaCGaagaggagttttCGCGttt               taggatggagtttttCGtatttttttttCGggttgttttgggattttttt               tttaagtttttttttCGgttgggttttgtattgtttttgggaCGttttgg               aattgggatttttaggtgtttttagtttttatttttttatgtataggtat               CGagatgtgttttatagtgggtttttgtttattCGattttttattttCGt               CGtttttCGttatttttttttttaatttagagagattagttCGgtttagg               ttgtttttttttttattttagttCGttttagggaaggaggCGtggttata               CGtataagttCGtttataaaggtgtagtattttatttttattttgaagg t                   gatagtttttggatg            
 
     [0069] In order to be able to amplify a part of the genomic segment shown after the bisulfite treatment, for example, the two primers with the sequences TATGTTAAATGGTATTGG and CATCCAAAAACTAT are used, with which defined fragments with a length of 1316 base pairs can be amplified. These amplificates serve as probes, which will be hybridized to oligonucleotides that have previously been bound to a solid phase, for example, CTACCCCGTAATA, whereby the cytosine to be detected is found at position 837 of the amplificate. The detection of the hybridization product is based on primer oligonucleotides fluorescently labeled with Cy3 or Cy5, which were used for the amplification. A hybridization reaction of the amplified DNA with the oligonucleotide occurs only if a methylated cytosine was present at this site in the bisulfite-treated DNA. Thus, the methylation state of the respective cytosine to be investigated decides the hybridization product.  
     EXAMPLE 6  
     Classification of a Chemical Substance in a Toxicity Class by Determination of the Methylation Pattern  
     [0070] In order to assign a chemical substance to a specific class on the basis of the methylation pattern, first an investigation must be made of the DNA methylation patterns in a group of exposed and a group of unexposed organisms, for example, experimental animals. The results are stored in a database and CpG dinucleotides are identified which are differently methylated in the two groups. Then the methylation pattern for the substance to be evaluated is compared with already known methylation patterns of other chemical substances. Indications of the properties of the substance to be investigated can be obtained from the toxicological properties of those chemical substances with similar methylation pattern.  
     [0071] The subject of the present invention is also a kit comprising a bisulfite-containing reagent, a set of primer oligonucleotides comprising at least two oligonucleotides, each of whose sequence of a segment at least 18 base pairs long corresponds to the base sequence of the genes to be investigated, or is complementary to them, for the production of amplificates, oligonucleotides and/or PNA oligomers, a control nucleic acid, as well as instructions for conducting and evaluating the described method.  
     [0072] Legends to Figures:  
     [0073]FIG. 1 
     [0074] Weighted matrix of the methylation state (fluorescent signal CG oligo×(fluorescent signal CG oligo+fluorescent signal TG oligo)−1) of 40 CpGs in untreated HT29-P208 cells (A) and TGF-b1-treated HT29-P208 cells (B). The numbers 1-3 denote 3 independent experiments (cell treatments and methylation analysis). Each horizontal row represents one CpG, whose methylation state is different, with a significance of p&lt;0.05, in the two groups analyzed. The darker gray tones correspond to a higher degree of methylation, while the lighter gray tones correspond to a smaller degree of methylation.  
     [0075]FIG. 2 
     [0076] Weighted matrix of the methylation state (fluorescent signal CG oligo×(fluorescent signal CG oligo+fluorescent signal TG oligo)−1) of 40 CpGs in untreated HT29-P208 cells (A) and IL-1b-treated HT29-P208 cells (B). The numbers 1-3 denote 3 independent experiments (cell treatments and methylation analysis). Each horizontal row represents one CpG, whose methylation state is different, with a significance of p&lt;0.05, in the two groups analyzed. The darker gray tones correspond to a higher degree of methylation, while the lighter gray tones correspond to a smaller degree of methylation.  
     [0077]FIG. 3 
     [0078] Quantitative analysis of the methylation state (fluorescent signal CG oligo×(fluorescent signal CG oligo+fluorescent signal TG oligo)−1) of 8 CpGs in untreated HT29-P208 cells (black columns), TGF-b1-treated (gray columns) and IL-1b-treated (white columns) HT29-P208 cells. CpGs, which are represented by the indicated oligo SEQ IDs were investigated from the following genes: TGF-a (A1, oligo SEQ IDs 6, 7; A2, oligo SEQ IDs 8, 9), EGFR (B1, oligo SEQ IDs 20, 21; B2, oligo SEQ IDs 22, 23), ANT1 (C1, oligo SEQ IDs 32, 33; C2, oligo SEQ IDs 34, 35) and E-cadherin (D1, oligo SEQ IDs 13, 14; D2, oligo SEQ IDs 15, 16). The numerical values of the y-axis show the methylation state, calculated as the quotient of the fluorescent signal of the CG oligos over the sum of the fluorescent signals of both the TG and CG oligos.  
     [0079]FIG. 4 
     [0080] Quantitative analysis of the methylation state (fluorescent signal CG oligo×(fluorescent signal CG oligo+fluorescent signal TG oligo)−1) of 4 CpGs in untreated HT29-P208 cells (black columns), trichostatin-treated (gray columns) and milrinone-treated (white columns) HT29-P208 cells. CpGs, which are represented by the indicated oligo SEQ IDs, were investigated from the following genes: EGFR (A1, oligo SEQ IDs 22, 23), ANT1 (B1, oligo SEQ IDs 32, 33; B2, oligo SEQ IDs 34, 35) and CDC25A (C1, oligo SEQ IDs 27, 28). The numerical values of the y-axis show the methylation state, calculated as the quotient of the fluorescent signal of the CG oligos over the sum of the fluorescent signals of both the TG and CG oligos.  
    
     
       
         1 
         
           
             35  
           
           
             1  
             2698  
             DNA  
             Homo Sapiens  
           
            1 

catgccaaat ggcactgggg cttcgtgtcg tgccacagcg tggaccgaaa atgcggacac     60 

atgcaggctg cctctcctcg caggcagaag ccacacgcag acctagaccc tttgcaccgc    120 

atccccttat tcaatcgcgc acccgccacc cttcgacagt tcctctccct ccaccccaac    180 

cccacgccgc gcgcgaggct ggccctttaa gagccccgcc ccgactccct cccccctcgc    240 

gtgactgcga gcccccgcgc cgggccgggg aatgggtcgg ctgggtggct gcgcgggcct    300 

ccggtccttc tcacgcaacg cctgggcacc gcgcctccgg gccaggtggg gcggggacgg    360 

gccgcctgac ctctgccccc tagagggatg tcgccggcgc acgcaagcta gccgggggta    420 

gggtgggggc tccgcgccag gtgccccctc cgtggtccct gggcccgagt ctttccgtgg    480 

ccccccgccg ccggatttct gtgctctgcc aatcaaagca ctagccaccc cgggagccaa    540 

gagggaccct caagggccgg tgggtcctgg ctggagggac cgcgcgttgc aatcagcact    600 

aaggcgatcc tagaggctgc gaggagccgc tagtgagcgc tcagcgagcc tgccccttcg    660 

ccatccattc cgatccttca atcaagaggc gcgaacctca gctagtcgcc cgggctctgg    720 

gggacaggtc cagccccgcg gcgcctctgg ccttccggcc cccgtgacct cagggctggg    780 

gtcgcagcgc ttctcacgcg agccgggact cagtaacccc gggaaggagg tcaccacggg    840 

gcagccccgc ccccgcctgc cgagtcctgg taggctgtag cgctggggag gcatctgcac    900 

gcccagcgtt ccagtgggtg caaaaatgac gaagaggagt ccccgcgccc caggatggag    960 

cttcccgtac cctctcttcg ggctgtcctg ggacttctcc ctcaagcccc ctcctcggct   1020 

gggttctgca ctgcccttgg gacgccttgg aattgggact tccaggtgtt cccagccctc   1080 

acccctctat gtacaggcac cgagatgtgt cccatagtgg gttcttgccc acccgacccc   1140 

ccacccccgc cgccctccgc cacctttctc tccaatccca gagagaccag cccggttcag   1200 

gctgcttctc cctccatctc agctcgctcc agggaaggag gcgtggccac acgtacaagc   1260 

ccgcctataa aggtgcagta cttcaccctc accctgaagg tgacagttct tggatgttcc   1320 

ctgatccttg tgatcccagg ctccaagagt ccacccttcc cagctcagct cagtacctca   1380 

ggtgagttgc tgggggactt ctggcttgcc ctttctctcc caataaaagg aacattttgg   1440 

tgcctccagg acttcttagg tagctacctg tctagcacct ccaaaaaggg aggctcagag   1500 

tgtttttagt gaccaggcag tctagccccc tagtggggaa actgaggcca ggggaagagg   1560 

aggacttgcc catggtccca cagctggtac cagacctcta gatacagatg gcatctcatt   1620 

caggacttca ggacccaggc tccagctcca tcccctagtg agtgtctccc tgcctaccct   1680 

ggggcttccc catcaaggcc acctggcagg ctggaatatg tgcagcccct ccctcaggct   1740 

ttctgatgac aggggcttct ccttgggtgg acagggtgga tggagggggt gggctgggtt   1800 

cttaccagct gtaccctgcc ctagcctaag aagctacccc tggcagattt taccctccta   1860 

agggtggctt gtcagtgctg agatgtccta gacagctggg acaatagagg cagatctgtg   1920 

caggagtccc aggcctttcc tatctcattg accatcttct ttgtcctttg ctgggagaca   1980 

atcagggtga cagattgcca actgcaggga gctggaaata ccagtcccta aaaactcacc   2040 

agtcacatct cccttggcct cctaccatct tacaaaggct gcaggtcctt gggataccca   2100 

ctgtgcagaa ggggacacca tagcacacca aagcctggca ctgtcccctg ttgactcagg   2160 

gatctagtgt gctttgatat ttagcccctc caggaagcct ccctccacta taatacttgt   2220 

ggtaggaacc atccatctcc ctgtcttgtg aggttctcct gtggggagcc taactggtaa   2280 

gactgtcagg ttccccacag cagatctggg ttttctcttc cctctggatc cagctgggta   2340 

ctctgaactg agagatcttg tcttaccctc tctcagatgt tgaaattgga ccccagaaaa   2400 

gtaaaatgtg cagtccaaga tcactttgac tagaatgttg gtctactgac ctctagtcca   2460 

gggtaacagg cagagatgcc tgatatgttg gagagagtgg tttatgaatt taaacaccct   2520 

ttttaggtca agcttacaga gaaagtattg cctcagtttc ctttcagttt agatccattc   2580 

ctgatttccc tgattccagt ctggggtttt cttacagcct agtgggaacc ttccatttat   2640 

tctctgctct ctggtaacct gcaaaagggg gaggtccaaa ctgttcattc attgagaa     2698 

 
           
             2  
             1316  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            2 

tatgttaaat ggtattgggg tttcgtgtcg tgttatagcg tggatcgaaa atgcggatat     60 

atgtaggttg ttttttttcg taggtagaag ttatacgtag atttagattt tttgtatcgt    120 

atttttttat ttaatcgcgt attcgttatt tttcgatagt tttttttttt ttattttaat    180 

tttacgtcgc gcgcgaggtt ggttttttaa gagtttcgtt tcgatttttt tttttttcgc    240 

gtgattgcga gttttcgcgt cgggtcgggg aatgggtcgg ttgggtggtt gcgcgggttt    300 

tcggtttttt ttacgtaacg tttgggtatc gcgttttcgg gttaggtggg gcggggacgg    360 

gtcgtttgat ttttgttttt tagagggatg tcgtcggcgt acgtaagtta gtcgggggta    420 

gggtgggggt ttcgcgttag gtgttttttt cgtggttttt gggttcgagt tttttcgtgg    480 

tttttcgtcg tcggattttt gtgttttgtt aattaaagta ttagttattt cgggagttaa    540 

gagggatttt taagggtcgg tgggttttgg ttggagggat cgcgcgttgt aattagtatt    600 

aaggcgattt tagaggttgc gaggagtcgt tagtgagcgt ttagcgagtt tgttttttcg    660 

ttatttattt cgatttttta attaagaggc gcgaatttta gttagtcgtt cgggttttgg    720 

gggataggtt tagtttcgcg gcgtttttgg tttttcggtt ttcgtgattt tagggttggg    780 

gtcgtagcgt tttttacgcg agtcgggatt tagtaatttc gggaaggagg ttattacggg    840 

gtagtttcgt tttcgtttgt cgagttttgg taggttgtag cgttggggag gtatttgtac    900 

gtttagcgtt ttagtgggtg taaaaatgac gaagaggagt tttcgcgttt taggatggag    960 

tttttcgtat ttttttttcg ggttgttttg ggattttttt tttaagtttt tttttcggtt   1020 

gggttttgta ttgtttttgg gacgttttgg aattgggatt tttaggtgtt tttagttttt   1080 

atttttttat gtataggtat cgagatgtgt tttatagtgg gtttttgttt attcgatttt   1140 

ttattttcgt cgtttttcgt tatttttttt tttaatttta gagagattag ttcggtttag   1200 

gttgtttttt tttttatttt agttcgtttt agggaaggag gcgtggttat acgtataagt   1260 

tcgtttataa aggtgtagta ttttattttt attttgaagg tgatagtttt tggatg       1316 

 
           
             3  
             531  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            3 

ggtttgtttg ggaggtaagg cggtaggcgt tgtagaattg atgggaattg tggtataggt     60 

gggaaatttg gtttaataaa ttttttattg atttagggga ttattttttt tgagttaagt    120 

tttggtaagc ggtcggcgaa atttataggt tttttttttg gttgcgtttt tagtttttag    180 

tttttttcgt tttagagatg ttttaggagc ggtttttcgg tgtaggtaac gggtgttcgg    240 

gcggtttcgt tcgtcgttta gagtttggaa gtcgttattg cggtttagga taattcggtt    300 

acgcggtcgg cgtcgatttc gtacgttgga gttcgttgtc gtacggcgtt ggtagtcggg    360 

ggtggtgttt gaagttaggc gttttttgtt ttttcgtcgg ttcgggtgtt cggttcgcgt    420 

cgttaggttt tgggatttta ggtcgtttcg tttagtagtt cgcgttttgt tcggtgcgtt    480 

tagcgttttc gttttttatt ttaaattttt attttttgtg tttttagggg g             531 

 
           
             4  
             19  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            4 

ggtttgtttg ggaggtaag                                                  19 

 
           
             5  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            5 

ccccctaaaa acacaaaa                                                   18 

 
           
             6  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            6 

gtttttttcg ttttagag                                                   18 

 
           
             7  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            7 

gttttttttg ttttagag                                                   18 

 
           
             8  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            8 

ttggtagtcg ggggtggt                                                   18 

 
           
             9  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            9 

ttggtagttg ggggtggt                                                   18 

 
           
             10  
             500  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            10 

gggtgaaaga gtgagtttta tttttaaaac gaataaataa aaaattttaa aaaataaaag     60 

aatttagtta agtgtaaaag ttttttttga ttttaggttt tagtgagtta tcggcggggt    120 

tgggattcga atttagtgga attagaatcg tgtaggtttt ataatttatt tagattttag    180 

taattttagg ttagagggtt atcgcgttta tgcgaggtcg ggtgggcggg tcgttagttt    240 

cgttttgggg aggggttcgc gttgttgatt ggttgtggtc ggtaggtgaa tttttagtta    300 

attagcggta cggggggcgg tgtttcgggg tttatttggt tgtagttacg tatttttttt    360 

tagtggcgtc ggaattgtaa agtatttgtg agtttgcgga agttagttta gattttagtt    420 

cgttttagtt cggttcgatt cgatcgtatt cggcgtttgt tttcgttcgg cgttttcggt    480 

tagttatggg tttttggagt                                                500 

 
           
             11  
             23  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            11 

gggtgaaaga gtgagtttta ttt                                             23 

 
           
             12  
             21  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            12 

actccaaaaa cccataacta a                                               21 

 
           
             13  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            13 

attagaatcg tgtaggtt                                                   18 

 
           
             14  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            14 

attagaattg tgtaggtt                                                   18 

 
           
             15  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            15 

gttagtttcg ttttgggg                                                   18 

 
           
             16  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            16 

gttagttttg ttttgggg                                                   18 

 
           
             17  
             966  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            17 

ggtgtttgat aagatttgaa ggattttcgg attttagagt attatttcgg aacgtttggt     60 

atttttgtcg cgcgggtacg gcgatttttt tagttgttag gttagttttt gattttcgcg    120 

aggggtttcg tagtgttgta gggggaggtt ggggattcga ataaaggagt agttttttcg    180 

tcggtgttat tattcgacgt tggttttaag gttcggttag tttgtttaaa gttggtataa    240 

gtttgttttg taaaataaaa gaagggaaag ggggaagggg attttggtat agatttggtt    300 

cgatttggat ataggttggg ttgtaagttc gcggggatcg ggtttagagg ggtagtgttg    360 

ggaacgtttt tttcggaaat taatttttta gggtatcgtt ttttttttat gcgtcgtttt    420 

attttcgtcg gagattaggt ttcgcggggg ttatcgtgtt tatcgtttcg cggtcgttgg    480 

ttttgggttt tcgttgttgg tttttttttt tttttttcgt attttttttt ttttttgttt    540 

ttttcgattt ttttttcgtc gtttggtttt tttttttttc gttttgtttt tcgcgtttcg    600 

gttcgcgcga gttagacgtt cgggtagttt tcggcgtagc gcggtcgtag tagttttttt    660 

ttttcgtacg gtgtgagcgt tcgtcgcgtc gaggcggtcg gagtttcgag ttagtttcgc    720 

ggtcgtcgtc gtttagatcg gacgataggt tatttcgtcg cgttcgttcg agttttcgtt    780 

tcgtcgttaa cgttataatt atcgcgtacg gttttttgat ttcgtttagt attgatcggg    840 

agagtcggag cgagtttttc ggggagtagc gatgcgattt ttcgggacgg tcggggtagc    900 

gtttttggcg ttgttggttg cgttttgttc ggcgagtcgg gttttggagg aaaagaaagg    960 

taaggg                                                               966 

 
           
             18  
             21  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            18 

ggtgtttgat aagatttgaa g                                               21 

 
           
             19  
             19  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            19 

cccttacctt tcttttcct                                                  19 

 
           
             20  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            20 

agtattgatc gggagagt                                                   18 

 
           
             21  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            21 

agtattgatt gggagagt                                                   18 

 
           
             22  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            22 

gagtttttcg gggagtag                                                   18 

 
           
             23  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            23 

gagttttttg gggagtag                                                   18 

 
           
             24  
             272  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            24 

agaagttgtt tattgattgg tggatttcgt ttggcgttaa ttaggaaagg ggggcggggt     60 

agtagttggt tttattgagt cgttattatc gcgaaaggtc ggtttggttg cgatagtttg    120 

ggtaagaggt gtaggtcggt ttggtttttt gttattcgga gttgggtaag cgggtgggag    180 

aatagcgaag atagcgtgag tttgggtcgt tgtttcgagt ttttcgttcg gttttttttg    240 

tcgattcgtt acgtttgttt ggatttaatt tt                                  272 

 
           
             25  
             20  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            25 

agaagttgtt tattgattgg                                                 20 

 
           
             26  
             20  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            26 

aaaattaaat ccaaacaaac                                                 20 

 
           
             27  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            27 

ttgttattcg gagttggg                                                   18 

 
           
             28  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            28 

ttgttatttg gagttggg                                                   18 

 
           
             29  
             186  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            29 

gtttaaggtt gtttgtgtta taaatacgcg gtttatatgt cgcggtgata cggtgttttt     60 

tgggttcggc gggatagata atatgaatgt gttttttaaa cgttttaagt tgtagggata    120 

gttttcggtt tagtttcgtt ttcggaagcg ttttcgtttt cgatgttttt tgtagttggg    180 

aggagg                                                               186 

 
           
             30  
             25  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            30 

gtttaaggtt gtttgtgtta taaat                                           25 

 
           
             31  
             19  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            31 

cctcctccca actacaaaa                                                  19 

 
           
             32  
             16  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            32 

ggtgatacgg tgtttt                                                     16 

 
           
             33  
             16  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            33 

ggtgatatgg tgtttt                                                     16 

 
           
             34  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            34 

tttgggttcg gcgggata                                                   18 

 
           
             35  
             18  
             DNA  
             Artificial Sequence  
             
               chemically treated genomic DNA (Homo sapiens)  
             
           
            35 

tttgggtttg gtgggata                                                   18