Table: 1 Description of Stage I-IV clones (EPITOPES)

Stage Description of the that are in- Size of Unigene # Serex Y/N Region of Antigen expression in any type of cancer (I-IV) frame with T7 10B the mRNA similarity clones peptide of AA 1F6 gi|18490914|gb|BC022506.1| 49 AA Hs.9222 N 165-213 Overexpressed in ovarian, nonsmall cell lung Homo sapiens, estrogen receptor carcinoma, pancreatic ductal cacinoma binding site associated,antigen,9 RCAS 2B3 gi|7023439|dbj|AK001891.1|, 10 AA Hs.528654 N 350-360 Not associated with cancer Homo sapiens cDNA FLJ11029 fis, clone PLACE1004156 2B4 gi|22042983|ref|XM_032391.3|, 212 AA Hs.446206 N 258-469 Expression levels are higher in myelogenous leukemia Homo sapiens similar to nuclear and lymphoblastic leukemia cells. autoantigenic sperm (histone- binding)(NASP) 2F7 gi|22042983|ref|XM_032391.3|, 15 AA Hs.446206 N 256-270 Expression levels are higher in myelogenous leukemia Homo sapiens similar to Nuclear and lymphoblastic leukemia cells. autoantigenic sperm protein (NASP) 2G4 gi|20987351|gb|BC030160.1| , 148 AA Hs.310621 N 1-148 eIF-5A2 sharing 82% identity of amino acid sequence Homo sapiens, eukaryotic translation with eIF-5A , is a candidate oncogene related to initiation factor 5A development of ovarian cancer.

3A9 gi|4507212|ref|NM_003135.1|, Homo 25 AA Hs.2943 N 119-143 Transcript generated by alternative splicing between sapiens signal recognition particle exon 14 of the Adenomatous polyposis coli gene and 19kDa (SRP19) SRP19 is observed and its expression is higher in Colorectal cancer 3C11 gi|16579884|ref|NM_000968.2| 68 AA Hs.186350 N 360-427 over-expression of L7a and L37 mRNA is confirmed in Homo sapiens ribosomal protein L4 prostate-cancer tissue samples. (RPL4) 4A11 gi|4557446|ref|NM_001270.1|,Homo 86 AA Hs.311553 N 107-192 Not associated with cancer sapiens chromodomain helicase DNA binding protein 1 (CHD1)

4H3 gi|20543465|ref|XM_045343.5|, 92 AA Hs.25812 N 433-524 Three different mutations in Nibrin gene, generating Homo sapiens Nijmegen breakage truncated or aberrant Nibrin transcripts were syndrome 1 (nibrin) observed in different cancer cell lines.

5C3 gi|20987351|gb|BC030160.1|, 118 AA Hs.310621 N 1-118 eIF-5A2 sharing 82% identity of amino acid sequence Homo sapiens, eukaryotic translation with eIF-5A , is a candidate oncogene related to initiation factor 5A development of ovarian cancer. 5C11 gi|535176|emb|X74818.1|HSAHNAKRS, 121 AA Hs.378738 N 393-512 Expression level of AHNAK is higher in melanoma, H.sapiens mRNA of AHNAK-related promyelocytic leukemia HL-60, osteosarcoma. sequence

5F8 gi|7662105|ref|NM_014711.1| , 150 AA Hs.279912 N 434-583 mRNA expression level of another antigen KIAA1416 is Homo sapiens KIAA0419 gene product up-regulated in colon cancer.

Table: 2 Description of Stage I-IV clones (MIMOTOPES) Size range of the Mimotopes >=5 amino acids

Stag Description of the Peptide sequences Size of Description of Unigene # Serex Region of similarity of AA Antigen expression e genes that are in of Mimotopes, the the sequences Y/N in any type of (I- Mimotope clones in-frame with T7 peptide that Mimotopes mRNA cancer IV) 10 B gene mimic clon es 2B9 gi|28837315|gb|BC0 VIVVLIAVISFPQNYTWL 18 AA gi|20141211|sp Hs.123022 N 172-185 Co-expression of 47588.1| Homo |P18825|A2AC_H Score = 24.8 bits (51), Expect = Beta adrenergic sapiens KIAA1363 UMAN, Alpha- 16 receptor and protein, mRNA 2C-adrenergic Identities = 10/14 (71%), cyclooxgenase 2 in receptor Positives = 10/14 (71%), Gaps = pulmonary (Alpha-2C 3/14 (21%) adenocarcinoma adrenoceptor) Query: 2 IVV--LI-AVISFP 12 (PAC). Beta (Subtype C4) IV LI AVISFP adrenergic Sbjct: 172 IVAVWLISAVISFP 185 receptor may serve as a upstream regulators of aracidonic acid and COX-2 mediated PAC growth. 2D7 gi|14041926|dbj|AK LRGTSGVQPPEIEQ 14 AA gi|32172435|sp Hs.1565 N 514-520 RING protein 027322.1|, Homo |P46934|NED4_H Score = 22.7 bits (46), Expect = Trim32 associated sapiens cDNA UMAN, 70 with skin FLJ14416 fis, Ubiquitin- Identities = 6/7 (85%), carcinogenesis has clone protein ligase Positives = 6/7 (85%) E3-ubiquitin HEMBA1005202, Nedd-4 Query: 8 QPPEIEQ 14 ligase properties highly similar QP EIEQ to SIGNAL Sbjct: 514 QPSEIEQ 520 RECOGNITION PARTICLE 68 KD PROTEIN.

2E7 gi|6330364|dbj|AB0 VLSALPEKNCNTVPFQPP 32 AA gi|34395825|sp Hs.339789 N 167-174 Protein-tyrosine 33020.1|, Homo EDLRYQHCSSRFLE |Q9H106|PTL2_H Score = 24.4 bits (50), Expect = phosphatase ( SAP- sapiens mRNA for UMAN Protein 21 1) is KIAA1194 protein tyrosine Identities = 7/8 (87%), overexpressed in phosphatase Positives = 8/8 (100%) gastrointestinal non-receptor Query: 2 LSALPEKN 9 cancer type substrate LSALPE+N 1-like 2 Sbjct: 167 LSALPERN 174 precursor

2H9 gi|21619682|gb|BC0 ELLRT 5 AA gi|20139301|sp N 407-411 Immunohistochemica 32762.1| , Homo |Q9Y446|PKP3_H Score = 18.9 bits (37), Expect = l localization of sapiens UMAN , 827 plakophilins optineurin, mRNA Plakophilin 3 Identities = 5/5 (100%), (PKP1, PKP2, PKP3, Positives = 5/5 (100%) and p0071) in Query b : 1 ELLRT 5 primary ELLRT oropharyngeal Sbjct c : 407 ELLRT 411 tumors 3B12 gi|21735624|ref|NM GQTSM 5 AA gi|729143|sp|P Hs.370771 N 144-147 mda-6 (p21) may _145690.1| , Homo 38936|CDN1_HUM Score = 16.8 bits (32), Expect = function as a sapiens tyrosine AN , Cyclin- 3595 negative regulator 3monooxygenase/try dependent Identities = 4/4 (100%), of melanoma ptophan 5- kinase Positives = 4/4 (100%) growth, monooxygenase inhibitor 1 Query: 2 QTSM 5 progression and activation (p21) (CDK- QTSM metastasis protein, zeta interacting Sbjct: 144 QTSM 147 polypeptide protein1) (YWHAZ), (Melanoma transcript variant differentiatio 2, mRNA. n associated protein 6 (MDA-6) 5D8 gi|22024583|gb|AC0 KKGPI 5 AA gi|20177863|sp Hs.153714 N 102-106 TNF-alpha 87376.5| , Homo |Q9BXJ2|CQT7_H Score = 18.5 bits (36), Expect = regulates sapiens UMAN 1109 expression of 11, clone RP11- ,Complement- Identities = 5/5 (100%), downstream 230O19, complete c1q and tumor Positives = 5/5 (100%) components of sequence necrosis Query: 1 KKGPI 5 complement system factor-related KKGPI and plays a role protein 7 Sbjct: 102 KKGPI 106 in energy precursor homeostatis where it is implicated in cachexia, obesity and insulin resistance. 4A4 gi|17028354|gb|BC0 AKVIMR 6 AA gi|5921908|sp| Hs.150595 N 138-142 all-trans-Retinoic 17483.1|BC017483 O43174|CP26_HU Score = 20.6 bits (41), Expect = acid-induced , Homo sapiens, MAN |, 255 expression and clone Cytochrome Identities = 5/5 (100%), regulation of IMAGE:3506553, P450 26 Positives = 5/5 (100%) retinoic acid 4- mRNA. (Retinoic Query: 2 KVIMR 6 hydroxylase acid- KVIMR (CYP26) in human metabolizingcy Sbjct: 138 KVIMR 142 promyelocytic tochrome) leukemia (P450RAI) 5A3 gi|15011541|gb|AF3 YACLKD 6 AA gi|1170473|sp| Hs.433103 N 351-355 CASP-3, CASP-4, 97158.1|AF397158 P42575|ICE2_HU Score = 20.2 bits (40), Expect = CASP-2 , Homo sapiens MAN 342 heterogeneously clone 11 pur ,Caspase-2 Identities = 5/5 (100%), coexpress in alpha-associated precursor Positives = 5/5 (100%) leukemic cell ribosomal RNA (CASP-2) (ICH- Query: 1 YACLK 5 lines gene, 1 protease) YACLK partial sequence Sbjct: 351 YACLK 355 2A3 gi|23271193|gb|BC0 QILFMDP 7 AA gi|729597|sp|P Hs.222405 N 242-246 Ionotropic and 36014.1| , Homo 39086|GLK1_HUM Score = 21.4 bits (43), Expect = metabotropic sapiens poly(A) AN , 142 glutamate receptor polymerase alpha, Glutamate Identities = 5/5 (100%), protein expression mRNA receptor, Positives = 5/5 (100%) in glioneuronal ionotropic Query: 1 QILFM 5 tumors from kainate 1 QILFM patients with precursor Sbjct: 242 QILFM 246 intractable epilepsy 4C10 gi|24756892|gb|AC0 LNTVNTLI 8 AA gi|13633936|sp Hs.416077 N 440-445 Not associated 08507.10| , Homo |Q9NPR2|SM4B_H Score = 21.8 bits (44), Expect = with cancer sapiens chromosome UMAN , 106 19 clone CTC- Semaphorin 4B Identities = 6/6 (100%), 448F2, complete Positives = 6/6 (100%) sequence Query: 1 NTVNTL 6 NTVNTL Sbjct: 440 NTVNTL 445 4D9 gi|21629397|gb|AC0 GNSILLIA 8 AA gi|2842764|sp| Hs.81874 N 3-10 The nuclear 99571.2| , Homo Q99735|GST2_HU Score = 21.4 bits (43), Expect = localisation of sapiens chromosome MAN , 140 GSTpi in tumour 1 clone RP11- Microsomal Identities = 7/8 (87%), cells is a useful 438H8, complete glutathione S- Positives = 7/8 (87%) prognosticator, sequence transferase 2 Query: 1 GNSILLIA 8 and may contribute (Microsomal GNSILL A to the selection GST-2) Sbjct: 3 GNSILLAA 10 of anticancer drugs forgynecological cancers. 2E11 gi|22004067|dbj|AP WDLKSEYS 8 AA gi|1710146|sp| Hs.386726 N 80-85 RGS4 is highly 005356.2| , Homo P49798|RGS4_HU Score = 21.8 bits (44), Expect = expressed in brain sapiens genomic MAN , 106 regions implicated DNA, chromosome Regulator of Identities = 6/6 (100%), in pathophysiology 8q23, clone: G-protein Positives = 6/6 (100%) of scizophrenia KB1198A4, complete signaling 4 Query: 3 LKSEYS 8 sequence. (RGS4) (RGP4) LKSEYS Sbjct: 80 LKSEYS 85 5G9 gi|20072204|gb|BC0 PGCSTTLS 8 AA gi|14423962|sp Hs.255596 N 940-947 Ubiquitin 26241.1| , Homo |O94966|UBPJ_H Score = 18.9 bits (37), Expect = carboxyl-terminal- sapiens ubiquitin- UMAN , 827 hydrolase L1 genes protein isopeptide Ubiquitin Identities = 6/8 (75%), cause autosomal ligase (E3), mRNA carboxyl- Positives = 7/8 (87%) dominant familial terminal Query: 1 PGCSTTLS 8 Parkinson disease. hydrolase 19 PGC+T LS Sbjct: 940 PGCTTLLS 947 4H4 gi|20072204|gb|BC0 PRCSTTLS 8 AA gi|6225843|sp| Hs.128433 N 156-160 Lipocalin-type 26241.1| , Homo O60760|PGD2_HU Score = 18.9 bits (37), Expect = prostaglandin D sapiens ubiquitin- MAN , 827 synthase (L-PGDS) protein isopeptide Glutathione- Identities = 5/5 (100%), has recently been ligase (E3), mRNA requiring Positives = 5/5 (100%) shown to prostaglandin Query: 3 CSTTL 7 be expressed in D synthase CSTTL human brain tumors Sbjct: 156 CSTTL 160 , breast tumors and in OVCA 2C7 gi|3152628|gb|AC00 GDRSQLWRK 9 AA gi|24211441|sp Hs.2442 N 720-725 Expression of 4744.1|AC004744 , |Q13443|AD09_H Score = 20.2 bits (40), Expect = ADAM-9 mRNA and Homo sapiens BAC UMAN , ADAM 342 protein in human clone GS1-465N13 9 precursor (A Identities = 5/6 (83%), breast cancer from 7, complete disintegrin Positives = 5/6 (83%) sequence and Query: 3 RSQLWR 8 metalloprotein R QLWR ase domain 9) Sbjct: 720 RDQLWR 725 2E1 gi|16160856|ref|XM KKQSSWYQI 9 AA gi|2498310|sp| Hs.1602 Y- 497-502 Higher DPD _007763.5|, Homo Q12882|DPYD_HU Breast Score = 21.8 bits (44), Expect = activity in sapiens myosin VA MAN Cancer 106 gastric cancer is (heavy polypeptide Dihydropyrimid Identities = 5/6 (83%), observed than in 12, myoxin) ine Positives = 6/6 (100%) colorectal cancer (MYO5A), mRNA dehydrogenase Query: 2 KQSSWY 7 [NADP+] KQ+SWY precursor Sbjct: 497 KQASWY 502 (DPD) (DHPDHase)(Dih ydrouracil dehydrogenase( Dihydrothymine dehydrogenase) 4A3 gi|16160856|ref|XM KKQSSWYQI 9 AA gi|2498310|sp| Hs.1602 Y- 497-502 Higher DPD _007763.5|, Homo Q12882|DPYD_HU Breast Score = 21.8 bits (44), Expect = activity in sapiens myosin VA MANDihydropyri Cancer 106 gastric cancer is (heavy polypeptide midine Identities = 5/6 (83%), observed than in 12, myoxin) dehydrogenase Positives = 6/6 (100%) colorectal cancer (MYO5A), mRNA [NADP+] Query: 2 KQSSWY 7 precursor KQ+SWY (DPD) Sbjct: 497 KQASWY 502 (DHPDHase)(Dih ydrouracil dehydrogenase) 4G8 gi|15778776|gb|AC0 PEGGTDASR 9 AA gi|13634077|sp Hs.307004 N 1912-1919 zonadhesin 12363.6| , Homo |Q9Y493|ZAN_HU Score = 18.9 bits (37), Expect = functions during sapiens BAC clone MAN 827 fertilization to RP11-438O12 from ,Zonadhesin Identities = 6/8 (75%), anchor the 2, complete Positives = 7/8 (87%) acrosomal shroud sequence Query: 2 EGGTDASR 9 to the zona EGGT+A R pellucida Sbjct: 1912 EGGTEAFR 1919

2E10 gi|20521965|dbj|AB ASFTLKLQS 9 AA gi|6226869|sp| Hs.90093 Y-colon 647-653 Expression of 051476.2| , Homo P34932|HS74_HU metasta Score = 21.8 bits (44), Expect = HSP70 is observed sapiens mRNA for MAN ,HEAT sis to 106 in human KIAA1689 protein, SHOCK 70 KDA lung, Identities = 6/7 (85%), hepatocellular partial cds PROTEIN 4 Stomach Positives = 7/7 (100%) carcinoma (HEAT SHOCK cancer, Query: 2 SFTLKLQ 8 70-RELATED Breast SFTLKL+ PROTEIN APG-2) Cancer Sbjct: 647 SFTLKLE 653

2D1 gi|4504522|ref|NM_ GGGSNGRTSV 10 AA gi|20137621|sp Hs.94262 N 140-148 EDD, the human 002157.1| , Homo |O95071|EDD_HU Score = 21.8 bits (44), Expect = orthologue of the sapiens heat shock MAN 105 hyperplastic discs 10kDa protein 1 ,Ubiquitin-- Identities = 7/9 (77%), tumour suppressor (chaperonin 10) protein ligase Positives = 9/9 (100%) gene, is amplified (HSPE1), mRNA EDD Query: 1 GGGSNGRTS 9 and overexpressed (Hyperplastic GGGS+GR+S in cancer discs protein Sbjct: 140 GGGSSGRSS 148 homolog)(hHYD) (Progestin induced protein)

5H6 gi|40849829|gb| NSFLMTSSKPR 11 AA gi|12643618|sp Hs.334087 N 694-699 BAI1 expression AAR95625| |O60242|BAI3_H Score = 20.6 bits (41), Expect = inhibit stromal NADH dehydrogenase UMAN ,Brain- 254 vascularization in subunit 4 specific Identities = 5/6 (83%), pulmonary angiogenesis Positives = 6/6 (100%) adenocarcinoma inhibitor 3 Query: 1 NSFLMT 6 precursor NS+LMT Sbjct: 694 NSYLMT 699

2C1 gi|23958536|gb|BC0 ACSSTVSFIWI 11 AA gi|33112422|sp Hs.160871 N 623-629 Functional 36216.1| , Homo |Q16827|PTPO_H Score = 21.8 bits (44), Expect = involvement of sapiens cullin 4B, UMAN 128 PTP-U2L in mRNA Receptor-type Identities = 6/7 (85%), apoptosis protein- Positives = 7/7 (100%) subsequent to tyrosine Query: 3 SSTVSFI 9 terminal phosphatase O SST+SFI differentiation of precursor Sbjct: 623 SSTISFI 629 monoblastoid (Glomerular leukemia cells epithelial protein 1) (Protein tyrosine phosphatase U2)(PTPase U2) (PTP-U2) 2G2 gi|25988997|gb|AF5 KKKKKKKRVGGPLQ 14 AA gi|20532388|sp Hs.363492 N 108-115 The expression of 41939.1| , His-3 |Q9NVP1|DD18_H Score = 27.4 bits (57), Expect = MrDb is induced integration vector UMAN , ATP- 2.8 upon proliferative pJHAM007, complete dependent RNA Identities = 8/8 (100%), stimulation of sequence helicase DDX18 Positives = 8/8 (100%) primary human (DEAD-box Query: 1 KKKKKKKR 8 fibroblasts as protein KKKKKKKR well as B cells 18)(Myc- Sbjct: 108 KKKKKKKR 115 and down-regulated regulated during terminal DEAD-box differentiation of protein) HL60 leukemia (MrDb) cells

4G9 gi|17136149|ref|NM GPVFICSSNCFKIT 14 AA gi|115892|sp|P Hs.75360 N 333-340 Expression of the _014708.2| , Homo 16870|CBPH_HUM Score = 24.4 bits (50), Expect = protein product of sapiens AN , 18 the PCPH proto- kinetochore Carboxypeptida Identities = 7/8 (87%), oncogene in human associated 1 se H precursor Positives = 8/8 (100%) tumor cell lines (KNTC1), mRNA (CPH) Query: 7 SSNCFKIT 14 (Carboxypeptid SSNCF+IT ase E) (CPE) Sbjct: 333 SSNCFEIT 340 (Enkephalin convertase) (Prohormone processing carboxypeptida se)

2E12 gi|22062543|ref|XM APFTCWPTVATNTWE 15 AA gi|128062|sp|P Hs.307734 N 167-175 NEP expression is _170670.1| , Homo 08473|NEP_HUMA Score = 23.5 bits (48), Expect = linked to sapiens putative N 32 malignant transmembrane ,Neprilysin Identities = 7/10 (70%), progression of protein; homolog (Neutral Positives = 7/10 (70%), Gaps = gliomas. of yeast Golgi endopeptidase) 1/10 (10%) membrane protein (NEP) Query: 6 WPTVATNTWE 15 Yif1p (Yip1p- (Enkephalinase WP VAT WE interacting ) (Common Sbjct: 167 WP-VATENWE 175 factor) (54TM), acute mRNA. lymphocytic leukemia antigen) (CALLA) (Neutral endopeptidase 24.11) (CD10) 1B5 gi|12654862|gb|BC0 TDQSSISPGNRKAPG 15 AA gi|6707734|sp| Hs.531251 N 64-70 Tumor necrosis 01275.1|BC001275 Q13077|TRA1_HU Score = 21.0 bits (42), Expect = factor receptor- , Homo sapiens MAN ,TNF 187 associated factor annexin A1, mRNA receptor Identities = 6/7 (85%), 1 gene associated Positives = 7/7 (100%) overexpression in factor 1 Query: 5 SISPGNR 11 B-cell chronic (TRAF1) SISPG+R lymphocytic Sbjct: 64 SISPGSR 70 leukemia

4B2 gi|23272851|gb|BC0 RIMGGGIQRETWISS 15 AA gi|20139133|sp Hs.318775 N 906-912 Oxysterol binding 35645.1| , Homo |Q9BZF3|ORP6_H Score = 21.8 bits (44), Expect = protein has been sapiens, Similar UMAN 104 implicated in the to RIKEN cDNA ,Oxysterol Identities = 5/7 (71%), regulation of 3830613O22 gene, binding Positives = 6/7 (85%) cellular clone protein- Query: 8 QRETWIS 14 cholesterol related QRE W+S metabolism. protein 6 Sbjct: 906 QREAWVS 912

5C6 gi|22797897|emb|AL ICGSWGKYNLWQSSSSK 17 AA gi|12644310|sp Hs.3059 N 250-257 A major component 160171.27| , |P53618|COPB_H Score = 22.3 bits (45), Expect = of the coat of Human DNA sequence UMAN,Coatomer 93 non-clathrin- from clone RP11- beta subunit Identities = 7/8 (87%), coated vesicles, 256E16 on (Beta-coat Positives = 7/8 (87%) beta-COP, is , protein) Query: 8 YNLWQSSS 15 required for complete sequence (Beta-COP) YNL QSSS transport of Sbjct: 250 YNLLQSSS 257 from ER to golgi compartment.

3C8 gi|24234687|ref|NM EILKPEGQHMKLRSEETS 18 AA gi|2493676|sp| Hs.1154 N 585-599 Oviduct specific _004134.3| , Homo Q12889|OGP_HUM Score = 24.4 bits (50), Expect = glycoproteins are sapiens heat shock AN ,Oviduct- 21 involved in 70kDa protein 9B specific Identities = 10/15 (66%), variety of roles (mortalin-2) glycoprotein Positives = 10/15 (66%), Gaps = during (HSPA9B), nuclear precursor 1/15 (6%) fertilization and gene encoding (Oviductal Query: 5 PEGQHMKLRSEE-TS 18 early embryonic mitochondrial glycoprotein) PEGQ MLR E TS development protein, mRNA. Sbjct: 585 PEGQTMPLRGENLTS 599 1H1 gi|11138930|gb|AF2 AKAESPGPPKRALFDWEV 154 AA gi|584908|sp| Hs.69771 N 27-35 Detection of 87967.1|AF287967, TAEIKAGAISPAQAPALR P00751|CFAB_H Score = 29.9 bits (63), Expect = complement C3 and Homo sapiens FPGAEAHSRFSPCRLGGW UMAN 7.4 factor B gene homeobox B7 RGAVSLSFSSLSSCIHST Complement Identities = 8/9 (88%), Positives expression in (HOXB7) gene, KGATEAPKALWRRRSHSL factor B = 8/9 (88%) normal colorectal partial cds GASAALFCPHLRSDPWSL precursor Query: 105 PWSLARPHG 113 mucosa, adenomas ARPHGQVFSPALALRSWP (C3/C5 PWSLARP G and carcinomas VALETEKWGHWVSLTLQL convertase) Sbjct: 27 PWSLARPQG 35 KAPGAPSHLK (Properdin factorB) (Glycine-rich beta glycoprotein) (GBG) (PBF2)

2F10 gi|21166212|gb|AC1 VQRGIGTIPSETIPVNRK 23 AA gi|118206|sp|P Hs.73893 N 264-270 Expression of 09584.2| , Homo RVNPP 14416|D2DR_HUM Score = 22.7 bits (46), Expect = dopamine receptors sapiens chromosome AN ,D(2) 56 and transporter in 3 clone RP11- dopamine Identities = 6/7 (85%), neuroendocrine 674P14, complete receptor Positives = 7/7 (100%) gastrointestinal sequence Query: 14 PVNRKRV 20 tumor cells PVNR+RV Sbjct: 264 PVNRRRV 270 5C12 gi|24430032|emb|AL VSWFPSWARSCGRQTPLG 28 AA gi|3915660|sp| Hs.512872 N 283-292 CYP2E1 protein is 939123.1|SCO939123 ATYKDTLLPV Q16850|CP51_HU Score = 24.4 bits (50), Expect = expressed in both , Streptomyces MAN, 17 tumour and normal coelicolor A3(2) Cytochrome Identities = 8/10 (80%), breast tissue with complete genome; P450 51A1 Positives = 8/10 (80%) an increased segment 20/29 (CYPLI) Query: 14 QTPLGATYKD 23 expression in (P450LI) QT L ATYKD breast tumors. (Sterol 14- Sbjct: 283 QTLLDATYKD 292 alpha demethylase) (Lanosterol 14-alpha demethylase) (LDM) (P450- 14DM)

2H5 gi|18606292|gb|BC0 DLQPPGRRWLPQQCPGSP 35 AA gi|116006|sp|P Hs.444324 N 40-49 Expression of 22865.1| GRCDASVPLWSDHLPSL 08575|CD45_HUM Score = 23.5 bits (48), Expect = leucocyte-common Homo sapiens ATP AN 41 antigen and large synthase, H+ ,Leukocyte Identities = 8/10 (80%), sialoglycoprotein transporting, common antigen Positives = 8/10 (80%) on leukemic cells mitochondrial F1 precursor (L- Query: 24 SVPLWSDHLP 33 in B-cell chronic complex, O subunit CA) SVPL SD LP lymphocytic (oligomycin Sbjct: 40 SVPLSSDPLP 49 leukemia and non- sensitivity Hodgkin's lymphoma conferring protein), mRNA 2F12 gi|10443350|emb|AL RGLGPLAAACGRSGGGGG 36 AA gi|8928460|sp| Hs.519209 N 2232-2244 Not associated 133264.10|AL133264 GGAGGTGSSNVNKKTPPN O75962|TRIO_HU Score = 31.2 bits (66), Expect = with cancer , Human DNA MAN , Triple 0.22 sequence from functional Identities = 11/13 (84%), clone RP3-369A17 domain protein Positives = 13/13 (100%) on chromosome (PTPRF Query: 13 SGGGGGGGAGGTG 25 6p22.1-22.3 interacting SGGGGGGG+GG+G Contains ESTs, protein) Sbjct: 2232 SGGGGGGGSGGSG 2244 STSs, GSSs and CpG islands

5C9 gi|15072584|emb|AL PMRCSCTMGEIQMQIHCG 37 AA gi|34395516|sp Hs.371602 N 409-417 A novel gene at 442003.8| , Human ARRRKAVPSSKDNVQSSA |O15085|ARHB_H Score = 23.1 bits (47), Expect = 11q23 named LARG DNA sequence from H UMAN ,Rho 72 for leukemia- clone RP11-324H6 guanine Identities = 7/9 (77%), associated Rho on chromosome 10, nucleotide Positives = 7/9 (77%) guanine nucleotide complete sequence exchange Query: 8 MGEIQMQIH 16 exchange factor factor 11 M EIQ QIH (GEF) has strong (PDZ-RhoGEF) Sbjct: 409 MPEIQEQIH 417 to several members of the Rho family of GEFs. Further, LARG was found to be fused with MLL in a patient with primary Rho GEF, Bcr, has been implicated in leukemia through a recurrent chromosomal translocation.

5F9 gi|18693518|gb|AC0 WRTTYISILNLAQFYYSL 48 AA gi|20139105|sp Hs.25051 N 471-492 Immunohistochemica 15911.8| , Homo ITVLKTFNWPGTVVHACN |Q99959|PKP2_H Score = 47.4 bits (111), Expect = l localization of sapiens chromosome PSTLGGQGRRIT UMAN 5e-06 plakophilins 17, clone RP11- ,Plakophilin 2 Identities = 19/22 (86%), (PKP1, PKP2, PKP3, 1094M14, complete Positives = 19/22 (86%) and p0071) in sequence Query: 27WPGTVVHACNPSTLGGQGRRIT primary 48 oropharyngeal WPG V HACNPSTLGGQG RIT tumors Sbjct:471WPGAVAHACNPSTLGGQGGRIT 492

Table: 3 Description of Stage II-IV clones (EPITOPES)

Stage Description of the genes that are Size of Unigene # Serex Y/N Region of Antigen expression in any type of cancer (II-IV) in-frame with T7 10B gene the mRNA similarit clones peptide y of AA 3H1 gi|12654010|gb|BC000805.1| 103 AA Hs.510265 N 140-243 The expression of casein kinase II (CK2) is Homo sapiens nuclear ubiquitous higher in neoplastic ovarian surface epithelium. casein kinase and cyclin-dependent kinase substrate, mRNA

Table: 4 Description of Stage II-IV clones (MIMOTOPES) Size range of the Mimotopes >=5 amino acids

Stage Description of the Peptide Size Description of the Unigene # Serex Region of similarity of AA Antigen expression (II- genes that are in sequences of of the sequences that Y/N in any type of IV) Mimotope clones the Mimotopes peptid Mimotopes mimic mRNA cancer clones that are in- e frame with T7 10 B gene 2C12 gi|15072584|emb|AL442 PMRCSCTMGEIQM 37 gi|2851534|sp|Q1372 Hs.516120 N 4-12 Not associated with 003.8| , Human DNA QIHCGARRRKAVP AA 4|GCS1_HUMAN Score = 24.0 bits (49), cancer sequence from clone SSKDNVQSSAH Mannosyl- Expect = 40 RP11-324H6 on oligosaccharide Identities = 7/9 (77%), chromosome glucosidase Positives = 8/9 (88%) 10,complete sequence (Processing A- Query: 18 GARRRKAVP 26 glucosidase I) G RRR+AVP Sbjct: 4 GERRRRAVP 12 2D12 gi|34783327|gb|BC0220 ILHLH 5 gi|128616|sp|P23975 Hs.78036 N 218-222 NET found in 49.2| , Homo sapiens AA |S6A2_HUMAN, Score = 17.6 bits (34), neuronal plasma cDNA clone Sodium-dependent Expect = 2425 membrane mediate the IMAGE:4291567, noradrenaline Identities = 4/5 (80%), removal of partial cds transporter Positives = 5/5 (100%) norepinephrine from (Norepinephrine Query: 1 ILHLH 5 extracellular space transporter) (NET) +LHLH limiting the Sbjct: 218 VLHLH 222 activation of adrenoceptors at noradrenergic synapses. 2G10 gi|16307467|gb|BC0102 WGFNERDRLSSIL 20 gi|13638201|sp|P412 Hs.274151 N 523-528 Hepatocellular 82.1| , Homo sapiens QQRCVTL AA 14|LIGA_HUMAN, Score = 24.0 bits (49), carcinoma associated leucine-rich PPR- Ligatin Expect = 29 tumor antigens motif containing, (Hepatocellular Identities = 6/6 (100%), provides potential mRNA carcinoma- Positives = 6/6 (100%) targets for associated antigen Query: 12 ILQQRC 17 immunotherapy of 56) ILQQRC hepatocellular Sbjct: 523 ILQQRC 528 carcinoma patients. 2G11 gi|7329921|emb|AL1173 VVSGFFSTFSL 11 gi|1705762|sp|P1356 Hs.521149 N 429-435 Mutation of CFTR is 79.14|HSJ563E14, AA 9|CFTR_HUMAN, Score = 21.8 bits (44), observed in Cystic Human DNA sequence Cystic fibrosis Expect = 128 Fibrosis from clone RP4-563E14 transmembrane Identities = 6/7 (85%), on chromosome 20 conductance Positives = 6/7 (85%) Contains the 5' of regulator (CFTR) Query: 5 FFSTFSL 11 the DATF1 gene FFS FSL encoding the death Sbjct: 429 FFSNFSL 435 associated transcription factor 1, the 5' end of a novel gene, ESTs, STSs, GSSs and four CpG islands, complete sequence.

2H8 gi|5714635|gb|AF15929 LTRPGHGQD 9 gi|2499758|sp|Q9272 Hs.19718 N 355-361 A potential role of 5.1|AF159295 , Homo AA 9|PTPU_HUMAN, Score = 19.3 bits (38), PCP-2 in cell-cell sapiens Receptor-type Expect = 748 recognition and serine/threonine protein-tyrosine Identities = 6/7 (85%), adhesion is protein kinase Kp78 phosphatase U Positives = 6/7 (85%) supported by its co- splice variant precursor (R-PTP- Query: 1 LTRPGHG 7 localization with CTAK75a mRNA U)(Protein-tyrosine LTRPG G cell adhesion phosphatase J) Sbjct: 355 LTRPGDG 361 molecules, such as (PTP-J) (Pancreatic catenin and E- carcinoma cadherin, at sites phosphatase 2) PCP- of cell-cell 2 contact.

4C5 gi|19683998|gb|BC0259 LYINEMKSKKL 11 gi|417216|sp|P33176 Hs.512922 N 592-599 Kinesin-1 links 57.1| AA |KINH_HUMAN, Score = 22.3 bits (45), neurofibromin and Homo sapiens coated Kinesin heavy chain Expect = 95 merlin in a common vesicle membrane (Ubiquitous kinesin Identities = 6/8 (75%), cellular pathway of protein, mRNA heavy chain) (UKHC) Positives = 8/8 (100%) neurofibromatosis Query: 1 LYINEMKS 8 LYI++MKS Sbjct: 592 LYISKMKS 599 4H6 gi|22773353|gb|AC0079 LPQCPSRGSL 10 gi|1352515|sp|P4874 Hs.235935 N 37-42 Altered expression 98.10| , Homo AA 5|NOV_HUMAN, NOV Score = 20.2 bits (40), of novH is sapiens chromosome protein homolog Expect = 414 associated with 18, clone RP11- precursor (NovH) Identities = 5/6 (83%), human adrenocortical 322E11, complete (Nephroblastoma Positives = 5/6 (83%) tumorigenesis sequence overexpressed gene Query: 2 PQCPSR 7 protein homolog) PQCP R Sbjct: 37 PQCPGR 42 5A2 gi|40788180|emb|AJ583 PGWDCRLPEAESC 23 gi|21759008|sp|Q96C Hs.256126 N 150-159 ML-IAP, a novel 821.2| , Homo RFLLSSRGED AA A5|BIR7_HUMAN, Score = 22.7 bits (46), inhibitor of sapiens mRNA for Baculoviral IAP Expect = 68 apoptosis , is ubiquitin specific repeat-containing Identities = 7/10 (70%), preferentially proteinase 40 (USP40 protein 7 (Kidney Positives = 9/10 (90%) expressed in human gene) inhibitor of Query: 12 SCRFLLSSRG 21 melanomas apoptosis protein) SC+FLL S+G (KIAP) (Melanoma Sbjct: 150 SCQFLLRSKG 159 inhibitor of apoptosis protein) (ML-IAP) (Livin) 5A7 gi|16508181|emb|AL138 KKMRTKM 7 gi|30580423|sp|Q8IX Hs.511876 N 14-19 A high expression 765.18| , Human DNA AA 29|FX16_HUMAN, F- Score = 20.6 bits (41), level of F-box sequence from clone box only protein 16 Expect = 310 protein, Skp2 is RP11-34E5 on Identities = 5/6 (83%), observed in diffuse chromosome 10, Positives = 6/6 (100%) large cell B complete sequence Query: 2 KMRTKM 7 lymphoma. KM+TKM Sbjct: 14 KMQTKM 19 5B9 gi|27469381|gb|BC0424 QIDSSFSIPWVVV 17 gi|126885|sp|P08235 Hs.331409 N 420-426 Glucocorticoid and 11.1| , Mus HGRS AA |MCR_HUMAN, Score = 22.3 bits (45), mineralocorticoid musculus, clone Mineralocorticoid Expect = 93 cross-talk with IMAGE:4014861, mRNA receptor (MR) Identities = 6/7 (85%), progesterone Positives = 7/7 (100%) receptor to induce Query: 3 DSSFSIP 9 focal adhesion and DSSFS+P growth inhibition in Sbjct: 420 DSSFSVP 426 breast cancer cells

5B12 gi|34996477|tpg|BK001 GGRRSLRKPQISF 18 gi|34223735|sp|Q084 Hs.414591 N 136-142 In human Y-79 418.1| , TPA: Homo FLFER AA 62|CYA2_HUMAN, Score = 24.4 bits (50), retinoblastoma sapiens metastasis Adenylate cyclase, Expect = 21 cells, associated in lung type II (ATP Identities = 6/7 (85%), corticotropin- adenocarcinoma pyrophosphate- Positives = 7/7 (100%) releasing hormone transcript 1 long lyase) (Adenylyl Query: 10 QISFFLF 16 (CRH) stimulates isoform, transcribed cyclase) Q+SFFLF adenylyl cyclase non-coding RNA, Sbjct: 136 QVSFFLF 142 activity and complete increases cyclic AMP sequence accumulation

5D6 gi|16741726|gb|BC0166 GIRVEPPTRTIS 12 gi|6226869|sp|P3493 Hs.90093 N 316-328 Expression of HSP70 60.1| , Homo sapiens AA 2|HS74_HUMAN, HEAT Score = 21.0 bits (42), in human heat shock 70kDa SHOCK 70 KDA Expect = 229 hepatocellular protein 8, transcript PROTEIN 4 (HEAT Identities = 6/9 (66%), carcinoma is induced variant 1, mRNA SHOCK 70-RELATED Positives = 8/9 (88%) by heat shock PROTEIN APG- Query: 3 RVEPPTRTI 11 2)(HSP70RY) RVEPP R++ Sbjct: 316 RVEPPLRSV 324

5E3 gi|40849693|gb|AY4953 RNRYSTARER 10 gi|2501463|sp|Q9300 Hs.77578 N 1356-1361 Oxidative 21.1| , Homo sapiens AA 8|FAFX_HUMAN, Score = 21.4 bits (43), Modifications and isolate V1-16 Probable ubiquitin Expect = 172 Down-regulation of mitochondrion, carboxyl-terminal Identities = 6/6 (100%), Ubiquitin Carboxyl- complete genome hydrolase FAF-X Positives = 6/6 (100%) terminal Hydrolase Query: 5 STARER 10 L1 Associated with STARER Idiopathic Sbjct: 1356 STARER 1361 Parkinson's Disease.

5H8 gi|13273214|gb|AAK178 GKRHIGGTDY 10 gi|41713338|sp|Q8N6 Correspond 21-25 The expression of 20| , AA 90|D119_HUMAN Beta- ing Score = 19.3 bits (38), human beta-defensin cytochrome c oxidase defensin 119 Unigene Expect = 550 genes in oral subunit I [Homo precursor (Beta- number is Identities = 5/5 (100%), squamous cell sapiens] defensin 19) (DEFB- not found Positives = 5/5 (100%) carcinomas(SCCs) was 19) Query: 1 GKRHI 5 demonstrated by in GKRHI situ hybridization. Sbjct: 21 GKRHI 25 5A4 gi|17149463|gb|AC0682 VVSQLTAEMRLE 12 gi|129825|sp|P05164 Hs.458272 N 23-29 Myeloperoxidase 28.8| , Homo sapiens AA |PERM_HUMAN, Score = 22.7 bits (46), immunoreactivity is chromosome 8, clone Myeloperoxidase Expect = 71 observed in adult RP11-539E17, complete precursor (MPO) Identities = 6/7 (85%), acute lymphoblastic sequence Positives = 7/7 (100%) leukemia Query: 5 LTAEMRL 11 LTAEM+L Sbjct: 23 LTAEMKL 29

5E7 gi|4885510|ref|NM_005 RACQRSTWKTKEG 21 gi|25453064|sp|Q9UP Hs.514335 N 192-199 JNK interacting 381.1| , Homo NGQTESSS AA T6|JIP3_HUMAN, C- Score = 23.1 bits (47), protein (JIP) can sapiens nucleolin jun-amino-terminal Expect = 51 inhibit JNK (NCL), mRNA kinase interacting Identities = 7/8 (87%), signaling pathway in protein 3 (JNK- Positives = 7/8 (87%) NPC cell interacting Query: 13 GNGQTESS 20 (nasopharyngeal protein 3) (JIP-3) GN QTESS carcinoma) Sbjct: 192 GNSQTESS 199