Supplementary information for

Coupled Two-Way Clustering Analysis of Breast Cancer and Colon Cancer Gene Expression Data

Gad Getz¹, Hilah Gal¹, Itai Kela¹, Daniel A. Notterman² and Eytan Domany¹
¹Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
²Department of Molecular Biology, Princeton University, Princeton, NJ 08544 and
Department of Pediatrics, Robert Wood Johnson Medical School, New Brunswick, NJ, 08903

Breast Cancer - PAL

G4, Figure 1
G46, G9
G21
G30, Figure 7

Breast Cancer - SAL

G10, Figure 2
G33, Figure 3
G36, Figure 4

Colon Cancer

G8, Figure 5
G3, Figure 6
G25, Figure 8
G24, Figure 9
G7, Figure 10
G12, Figure 11

Breast Cancer - PAL

G4

1	1593	X-BOX BINDING PROTEIN 1
2	1594	"HEPATOCYTE NUCLEAR FACTOR 3, ALPHA"
3	1595	GATA-BINDING PROTEIN 3
4	1596	GATA-BINDING PROTEIN 3
5	1597	GATA-BINDING PROTEIN 3
6	1598	GATA-BINDING PROTEIN 3
7	1599	ESTROGEN RECEPTOR 1
8	1600	ESTROGEN RECEPTOR 1
9	1601	ANNEXIN XXXI
10	1602	ANNEXIN XXXI

G9

1	647	"ESTS, WEAKLY SIMILAR TO W01A11.2 GENE PRODUCT [C.ELEGANS]"
2	658	78946
3	659	"FATTY ACID BINDING PROTEIN 4, ADIPOCYTE"
4	660	"FATTY ACID BINDING PROTEIN 4, ADIPOCYTE"
5	665	GLUTATHIONE PEROXIDASE 3 (PLASMA)
6	667	"ALCOHOL DEHYDROGENASE 2 (CLASS I), BETA POLYPEPTIDE"
7	668	AQUAPORIN 7
8	669	484535
9	670	LIPOPROTEIN LIPASE
10	671	GLYCEROL-3-PHOSPHATE DEHYDROGENASE 1 (SOLUBLE)
11	672	"RETINOL-BINDING PROTEIN 4, INTERSTITIAL"
12	673	"INTEGRIN, ALPHA 7"
13	674	85660

G21

1	1709	418240
2	1710	KIAA0130 GENE PRODUCT
3	1711	ERBB-2 RECEPTOR PROTEIN-TYROSINE KINASE PRECURSOR
4	1712	STEROIDOGENIC ACUTE REGULATORY PROTEIN RELATED
5	1713	ERBB2-POLYA
6	1714	V-ERB-B2 AVIAN ERYTHROBLASTIC LEUKEMIA VIRAL ONCOGENE HOMOLOG 2 (NEURO/GLIOBLASTOMA DERIVED ONCOGENE HOMOLOG)
7	1715	V-ERB-B2 AVIAN ERYTHROBLASTIC LEUKEMIA VIRAL ONCOGENE HOMOLOG 2 (NEURO/GLIOBLASTOMA DERIVED ONCOGENE HOMOLOG)
8	1716	ERBB2
9	1717	GROWTH FACTOR RECEPTOR-BOUND PROTEIN 7
10	1718	68400
11	1719	68400
12	1720	"SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN, SUBFAMILY E, MEMBER 1"

G30

1	856	"HUMAN UBIQUITIN CARRIER PROTEIN (E2-EPF) MRNA, COMPLETE CDS"
2	857	"ESTS, HIGHLY SIMILAR TO MITOTIC KINESIN-LIKE PROTEIN-1 [H.SAPIENS]"
3	859	"CELL DIVISION CYCLE 20, S.CEREVISIAE HOMOLOG"
4	860	"HOMO SAPIENS MRNA FOR KIAA0788 PROTEIN, PARTIAL CDS"
5	861	"HOMO SAPIENS HPV16 E1 PROTEIN BINDING PROTEIN MRNA, COMPLETE CDS"
6	862	"CENTROMERE PROTEIN F (350/400KD, MITOSIN)"
7	863	782283
8	865	CYCLIN A2
9	866	"HOMO SAPIENS MRNA FOR CDC2 DELTA T, COMPLETE CDS"
10	867	PROTEIN KINASE MITOGEN- ACTIVATED 13
11	868	POLO (DROSOPHIA)-LIKE KINASE
12	869	"HUMAN MRNA FOR KIAA0074 GENE, PARTIAL CDS"
13	870	BUDDING UNINHIBITED BY BENZIMIDAZOLES 1 (YEAST HOMOLOG)
14	871	MINICHROMOSOME MAINTENANCE DEFICIENT (S. CEREVISIAE) 4
15	874	FORKHEAD (DROSOPHILA)-LIKE 16

G46

1	827	APOPTOSIS INHIBITOR 4 (SURVIVIN)
2	830	258761
3	832	KIAA0101 GENE PRODUCT
4	846	"MINICHROMOSOME MAINTENANCE DEFICIENT (MIS5, S. POMBE) 6"
5	850	REPLICATION FACTOR C (ACTIVATOR 1) 4 (37KD)
6	851	V-MYB AVIAN MYELOBLASTOSIS VIRAL ONCOGENE HOMOLOG-LIKE 2
7	853	CDC28 PROTEIN KINASE 2
8	854	CDC28 PROTEIN KINASE 2
9	855	PITUITARY TUMOR-TRANSFORMING 1
10	856	"HUMAN UBIQUITIN CARRIER PROTEIN (E2-EPF) MRNA, COMPLETE CDS"
11	857	"ESTS, HIGHLY SIMILAR TO MITOTIC KINESIN-LIKE PROTEIN-1 [H.SAPIENS]"
12	858	TROPHININ-ASSISTING PROTEIN (TASTIN)
13	859	"CELL DIVISION CYCLE 20, S.CEREVISIAE HOMOLOG"
14	860	"HOMO SAPIENS MRNA FOR KIAA0788 PROTEIN, PARTIAL CDS"
15	861	"HOMO SAPIENS HPV16 E1 PROTEIN BINDING PROTEIN MRNA, COMPLETE CDS"
16	862	"CENTROMERE PROTEIN F (350/400KD, MITOSIN)"
17	863	782283
18	864	POLYMYOSITIS/SCLERODERMA AUTOANTIGEN 1 (75KD)
19	865	CYCLIN A2
20	866	"HOMO SAPIENS MRNA FOR CDC2 DELTA T, COMPLETE CDS"
21	867	PROTEIN KINASE MITOGEN- ACTIVATED 13
22	868	POLO (DROSOPHIA)-LIKE KINASE
23	869	"HUMAN MRNA FOR KIAA0074 GENE, PARTIAL CDS"
24	870	BUDDING UNINHIBITED BY BENZIMIDAZOLES 1 (YEAST HOMOLOG)
25	871	MINICHROMOSOME MAINTENANCE DEFICIENT (S. CEREVISIAE) 4
26	872	FLAP STRUCTURE-SPECIFIC ENDONUCLEASE 1
27	873	236142
28	874	FORKHEAD (DROSOPHILA)-LIKE 16
29	876	SMALL NUCLEAR RIBONUCLEOPROTEIN POLYPEPTIDES B AND B1
30	877	PROLIFERATING CELL NUCLEAR ANTIGEN
31	878	PROLIFERATING CELL NUCLEAR ANTIGEN
32	880	"NON-METASTATIC CELLS 1, PROTEIN (NM23A) EXPRESSED IN"
33	881	"HUMAN MRNA FOR KIAA0098 GENE, PARTIAL CDS"

Breast Cancer - SAL

G10

1	257	R01070	"ESTS, HIGHLY SIMILAR TO (DEFLINE NOT AVAILABLE 4929675) [H.SAPIENS] "
2	712	AA187002	625764
3	1474	AA699427	FRUCTOSE-BISPHOSPHATASE 1
4	1475	AA701655	HUMAN ENDOGENOUS RETROVIRUS ENVELOPE REGION MRNA (PL1)
5	1476	W90128	X-BOX BINDING PROTEIN 1
6	1477	H72474	GATA-BINDING PROTEIN 3
7	1478	R31441	GATA-BINDING PROTEIN 3
8	1479	R31441	GATA-BINDING PROTEIN 3
9	1480	AA058828	GATA-BINDING PROTEIN 3
10	1489	N74131	"HUMAN SECRETORY PROTEIN (P1.B) MRNA, COMPLETE CDS "
11	1521	AA029948	470105
12	1528	H95792	"ACYL-COENZYME A DEHYDROGENASE, SHORT/BRANCHED CHAIN "
13	1535	T95267	"ESTS, WEAKLY SIMILAR TO TUMOROUS IMAGINAL DISCS PROTEIN TID56 HOMOLOG [H.SAPIENS] "
14	1537	H99588	LYMPHOID NUCLEAR PROTEIN RELATED TO AF4
15	1538	AA428477	NUCLEOPORIN 88KD

G33

1	735	AA448261	HIGH-MOBILITY GROUP (NONHISTONE CHROMOSOMAL) PROTEIN ISOFORMS I AND Y
2	746	AA455800	"GAMMA-GLUTAMYL HYDROLASE (CONJUGASE, FOLYLPOLYGAMMAGLUTAMYL HYDROLASE) "
3	756	AA443998	"MUTT (E. COLI) HUMAN HOMOLOG (8-OXO-7,8-DIHYDROGUANOSINE TRIPHOSPHATASE) "
4	757	AA633549	RIBONUCLEOTIDE REDUCTASE M1 POLYPEPTIDE
5	761	AA460685	APOPTOSIS INHIBITOR 4 (SURVIVIN)
6	763	AA701929	BYSTIN-LIKE
7	767	AA026682	TOPOISOMERASE (DNA) II ALPHA (170KD)
8	770	AA504348	"ESTS, HIGHLY SIMILAR TO TOPOISOMERASE II ALPHA {C-TERMINAL} [H.SAPIENS] "
9	778	AA663995	"MINICHROMOSOME MAINTENANCE DEFICIENT (MIS5, S. POMBE) 6 "
10	781	AA428252	ENHANCER OF ZESTE (DROSOPHILA) HOMOLOG 2
11	782	N93924	REPLICATION FACTOR C (ACTIVATOR 1) 4 (37KD)
12	783	AA456878	V-MYB AVIAN MYELOBLASTOSIS VIRAL ONCOGENE HOMOLOG-LIKE 2
13	785	AA010065	CDC28 PROTEIN KINASE 2
14	786	AA292964	CDC28 PROTEIN KINASE 2
15	787	AA430032	PITUITARY TUMOR-TRANSFORMING 1
16	788	AA464019	"HUMAN UBIQUITIN CARRIER PROTEIN (E2-EPF) MRNA, COMPLETE CDS "
17	789	AA452513	"ESTS, HIGHLY SIMILAR TO MITOTIC KINESIN-LIKE PROTEIN-1 [H.SAPIENS] "
18	792	AA676460	"HOMO SAPIENS MRNA FOR KIAA0788 PROTEIN, PARTIAL CDS "
19	793	AA630784	"HOMO SAPIENS HPV16 E1 PROTEIN BINDING PROTEIN MRNA, COMPLETE CDS "
20	794	AA701455	"CENTROMERE PROTEIN F (350/400KD, MITOSIN) "
21	796	AA458994	POLYMYOSITIS/SCLERODERMA AUTOANTIGEN 1 (75KD)
22	798	AA598974	"HOMO SAPIENS MRNA FOR CDC2 DELTA T, COMPLETE CDS "
23	799	AA157499	PROTEIN KINASE MITOGEN- ACTIVATED 13
24	800	AA629262	POLO (DROSOPHIA)-LIKE KINASE
25	803	AA485983	MINICHROMOSOME MAINTENANCE DEFICIENT (S. CEREVISIAE) 4
26	804	AA620553	FLAP STRUCTURE-SPECIFIC ENDONUCLEASE 1
27	806	AA129552	FORKHEAD (DROSOPHILA)-LIKE 16
28	810	AA450264	PROLIFERATING CELL NUCLEAR ANTIGEN
29	819	N69491	292933
30	830	AA504348	"ESTS, HIGHLY SIMILAR TO TOPOISOMERASE II ALPHA {C-TERMINAL} [H.SAPIENS] "
31	839	AA434411	770898
32	845	AA448659	CELL DIVISION CYCLE 25B
33	846	T52362	"CHLORIDE CHANNEL, NUCLEOTIDE-SENSITIVE, 1A "
34	1150	AA115761	490718
35	1346	AA419176	"SOLUTE CARRIER FAMILY 7 (CATIONIC AMINO ACID TRANSPORTER, Y+ SYSTEM), MEMBER 5 "
36	1407	AA056377	509462

G36

1	65	AA026831	"HOMO SAPIENS KDR/FLK-1 PROTEIN MRNA, COMPLETE CDS "
2	126	W88788	H FACTOR (COMPLEMENT)-LIKE 1
3	252	R95691	CAG REPEAT CONTAINING (GLIA-DERIVED NEXIN I ALPHA)
4	253	N57754	CAG REPEAT CONTAINING (GLIA-DERIVED NEXIN I ALPHA)
5	272	AA459922	METHYL-CPG BINDING DOMAIN PROTEIN 1
6	499	H61303	236142
7	511	N48737	277463
8	556	AA227594	"MAL, T-CELL DIFFERENTIATION PROTEIN "
9	577	R99105	201440
10	805	H61303	236142
11	840	AA126951	"ESTS, HIGHLY SIMILAR TO (DEFLINE NOT AVAILABLE 4877775) [H.SAPIENS] "
12	863	N72115	"CYCLIN-DEPENDENT KINASE INHIBITOR 2C (P18, INHIBITS CDK4) "
13	1005	AA283864	GLUTAREDOXIN (THIOLTRANSFERASE)
14	1018	AA055945	"CD3D ANTIGEN, DELTA POLYPEPTIDE (TIT3 COMPLEX) "
15	1097	AA463946	PIGMENT EPITHELIUM-DERIVED FACTOR
16	1098	AA485674	811095
17	1143	AA074117	RECOVERIN
18	1198	AA453271	795367
19	1200	T60269	"SUPEROXIDE DISMUTASE 2, MITOCHONDRIAL "
20	1202	N94612	309803
21	1213	AA029776	"CYTOCHROME P450, SUBFAMILY I (DIOXIN-INDUCIBLE), POLYPEPTIDE 1 (GLAUCOMA 3, PRIMARY INFANTILE) "
22	1215	N92699	306420
23	1264	N92697	"ESTS, WEAKLY SIMILAR TO !!!! ALU SUBFAMILY SQ WARNING ENTRY !!!! [H.SAPIENS] "
24	1434	R93185	275798
25	1440	N77806	NEBULETTE
26	1442	AA042878	486828
27	1443	AA042878	486828
28	1465	H53479	202658
29	1466	H53479	202658
30	1492	H58234	204483
31	1507	AA460368	"HOMO SAPIENS BREAST CANCER PUTATIVE TRANSCRIPTION FACTOR (ZABC1) MRNA, COMPLETE CDS "
32	1510	R07647	HEREDITARY HEMOCHROMOTOSIS
33	1529	H41908	"CYTOCHROME P450, SUBFAMILY IIB (PHENOBARBITAL-INDUCIBLE), POLYPEPTIDE 6 "
34	1549	W61100	B-CELL CLL/LYMPHOMA 2
35	1552	AA448277	FORKHEAD (DROSOPHILA) HOMOLOG 1 (RHABDOMYOSARCOMA)
36	1555	AA045481	487929

Colon Cancer

G3

1	16	D13902	Human mRNA for peptide YY, complete cds
2	28	D30758	Human mRNA for KIAA0050 gene, complete cds
3	35	D49490	Human mRNA for protein disulfide isomerase-related protein (PDIR), complete cds
4	60	H19272	yn50d10.s1 Homo sapiens cDNA clone 171859 3'
5	70	H27202	yl15f10.s1 Homo sapiens cDNA clone 158347 3'
6	84	H46934	yo15h09.s1 Homo sapiens cDNA clone 178049 3'
7	112	H70609	yu18b07.s1 Homo sapiens cDNA clone 234133 3' similar to contains MER22 repetitive element ;
8	117	H85835	ys95a03.s1 Homo sapiens cDNA clone 222508 3'
9	166	L13268	Homo sapiens N-methyl-d-aspartate receptor (NR1-3) mRNA, 3' end
10	247	M28650	Human excision repair protein (ERCC-1) mRNA, complete cds. cDNA clone pcDE
11	347	R16153	ya48f08.s1 Homo sapiens cDNA clone 53165 3'
12	361	R39010	yd08d06.s1 Homo sapiens cDNA clone 25204 3'
13	368	R41866	yg12f04.s1 Homo sapiens cDNA clone 31854 3'
14	386	R49565	yg68b12.s1 Homo sapiens cDNA clone 38251 3'
15	406	R56052	yg91c01.s1 Homo sapiens cDNA clone 40877 3'
16	413	R61523	yh16d01.s1 Homo sapiens cDNA clone 37998 3' similar to gb:U02389 MITOCHONDRIAL LON PROTEASE HOMOLOG PRECURSOR (HUMAN);
17	428	R72164	yj88b08.s1 Homo sapiens cDNA clone 155799 3'
18	459	T40653	ya07c05.s1 Homo sapiens cDNA clone 60776 3' similar to SP:PLC_HUMAN P01243 LACTOGEN PRECURSOR ,
19	536	T66307	yc78d05.s1 Homo sapiens cDNA clone 22190 3' similar to gb:M11717_rna1 HEAT SHOCK 70 KD PROTEIN 1 (HUMAN);
20	611	U19261	Human Epstein-Barr virus-induced protein mRNA, complete cds
21	641	X04500	Human gene for prointerleukin 1 beta
22	665	X16351	Human testis mRNA for a sex hormone-binding related protein (SHBGgrp)
23	678	X52229	Human mRNA for transmembrane epithelial tumour mucin antigen
24	685	X53683	Human LAG-1 mRNA
25	709	X69550	H.sapiens mRNA for rho GDP-dissociation Inhibitor 1
26	734	X83535	H.sapiens mRNA for membrane-type matrix metalloproteinase
27	740	X86779	H.sapiens mRNA for FAST kinase

G7

1	246	M28214	Homo sapiens GTP-binding protein (RAB3B) mRNA, complete cds
2	322	M91670	Human ubiquitin carrier protein (E2-EPF) mRNA, complete cds
3	570	T96816	ye51a11.s1 Homo sapiens cDNA clone 121244 3' similar to gb:M88468 MEVALONATE KINASE (HUMAN);
4	575	T99498	ye64h10.s1 Homo sapiens cDNA clone 122563 3'
5	680	X52426	H.sapiens mRNA for cytokeratin 13
6	699	X60489	Human mRNA for elongation factor-1-beta
7	754	Z17240	Homo sapiens for mRNA encoding HMG2B

G8

1	10	D10511	"""Human gene for mitochondrial acetoacetyl-CoA thiolase, exon 12"" "
2	12	D10523	"""Human mRNA for 2-oxoglutarate dehydrogenase, complete cds"""
3	13	D10537	"""Human mRNA for major structural protein of myelin, complete cds"" "
4	22	D13168	"""Human gene for endothelin-B receptor (hET-BR), exon 7"" "
5	24	D13626	"""Human mRNA for KIAA0001 gene, complete cds"" "
6	44	D14662	"""Human mRNA for KIAA0106 gene, complete cds"" "
7	58	D16294	"""Human mRNA for mitochondrial 3-oxoacyl-CoA thiolase, complete cds"" "
8	140	D42047	"""Human mRNA for KIAA0089 gene, partial cds"" "
9	183	J02854	"""Human 20-kDa myosin light chain (MLC-2) mRNA, complete cds"" "
10	209	J04080	"""Human complement component C1r mRNA, complete cds"" "
11	252	L02785	"""Homo sapiens colon mucosa-associated (DRA) mRNA, complete cds"" "
12	282	L07648	"""Human MXI1 mRNA, complete cds"" "
13	301	L11708	"""Human 17 beta hydroxysteroid dehydrogenase type 2 mRNA, complete cds"" "
14	352	L20852	"""Human leukemia virus receptor 2 (GLVR2) mRNA, complete cds"" "
15	353	L20859	"""Human leukemia virus receptor 1 (GLVR1) mRNA, complete cds"" "
16	396	L34060	"""Homo sapiens cadherin-8 mRNA, complete cds"" "
17	449	L41143	"""Homo sapiens expressed pseudo TCTA mRNA at t(1;3) translocation site, complete cds"" "
18	529	M22995	"""Human ras-related protein (Krev-1) mRNA, complete cds"" "
19	621	M36634	"""Human vasoactive intestinal peptide (VIP) mRNA, complete cds"" "
20	633	M54927	"""Human myelin proteolipid protein mRNA, complete cds"" "
21	679	M63391	"""Human desmin gene, complete cds"" "
22	682	M63603	"""Human phospholamban mRNA, complete cds"" "
23	692	M64497	"""Human apolipoprotein AI regulatory protein (ARP-1) mRNA, complete cds"" "
24	700	M65254	"""Protein phosphatase 2A 65 kDa regulatory subunit-beta mRNA, complete cds"" "
25	706	M69066	"""Human moesin mRNA, complete cds"" "
26	717	M74096	"""Human long chain acyl-CoA dehydrogenase (ACADL) mRNA, complete cds"" "
27	727	M76378	"""Human cysteine-rich protein (CRP) gene, exons 5 and 6"" "
28	753	M82962	"""Human N-benzoyl-L-tyrosyl-p-amino-benzoic acid hydrolase alpha subunit (PPH alpha) mRNA, complete cds"" "
29	755	M83186	"""Human cytochrome c oxidase subunit VIIa (COX7A) muscle isoform mRNA, complete cds"" "
30	769	M85289	"""Human heparan sulfate proteoglycan (HSPG2) mRNA, complete cds"" "
31	822	M95787	"""Human 22kDa smooth muscle protein (SM22) mRNA, complete cds"" "
32	831	M97287	"""Human MAR/SAR DNA binding protein (SATB1) mRNA, complete cds"" "
33	833	M97496	"""Homo sapiens guanylin mRNA, complete cds"" "
34	963	U13395	"""Human oxidoreductase (HHCMA56) mRNA, complete cds"" "
35	997	U17077	"""Human BENE mRNA, partial cds"" "
36	1033	U20938	"""Human lymphocyte dihydropyrimidine dehydrogenase mRNA, complete cds"" "
37	1108	U34038	"""Human proteinase-activated receptor-2 mRNA, complete cds"" "
38	1150	X05610	Human mRNA for type IV collagen alpha (2) chain
39	1152	X06256	Human mRNA for fibronectin receptor alpha subunit
40	1171	X07767	Human mRNA for cAMP-dependent protein kinase catalytic subunit type alpha (EC 2.7.1.37)
41	1194	X15880	Human mRNA for collagen VI alpha-1 C-terminal globular domain
42	1195	X15882	Human mRNA for collagen VI alpha-2 C-terminal globular domain
43	1201	X16354	Human mRNA for transmembrane carcinoembryonic antigen BGPa (formerly TM1-CEA)
44	1217	X51405	Human mRNA for carboxypeptidase E (EC 3.4.17.10)
45	1236	X53416	Human mRNA for actin-binding protein (filamin) (ABP-280)
46	1240	X54162	Human mRNA for a 64 Kd autoantigen expressed in thyroid and extra-ocular muscle
47	1264	X57348	H.sapiens mRNA (clone 9112)
48	1315	X64559	H.sapiens mRNA for tetranectin
49	1345	X68277	H.sapiens CL 100 mRNA for protein tyrosine phosphatase
50	1384	X74295	H.sapiens mRNA for alpha 7B integrin
51	1487	X86693	H.sapiens mRNA for hevin like protein
52	1490	X87159	H.sapiens mRNA for beta subunit of epithelial amiloride-sensitive sodium channel
53	1543	Z22535	H.sapiens ALK-3 mRNA
54	1549	Z24727	"""H.sapiens tropomyosin isoform mRNA, complete CDS"" "
55	1592	Z49269	H.sapiens gene for chemokine HCC-1

G12

1	338	R00453	ye72d11.s1 Homo sapiens cDNA clone 123285 3'
2	474	T49945	ya99e09.s1 Homo sapiens cDNA clone 69832 3' similar to gb:X00570 APOLIPOPROTEIN C-I PRECURSOR (HUMAN)
3	636	X02530	Human mRNA for gamma-interferon inducible early response gene (with homology to platelet proteins)
4	673	X17668	Human mRNA for indoleamine 2,3-dioxygenase
5	714	X72755	H.sapiens Humig mRNA

G24

1	147	K01144	Human major histocompatibility class II antigen gamma chain mRNA, complete cds
2	221	M18737	Human Hanukah factor serine protease (HuHF) mRNA, complete cds
3	222	M18737	Human Hanukah factor serine protease (HuHF) mRNA, complete cds
4	302	M79463	Human PML-2 mRNA, complete CDS
5	524	T62558	yc04f07.s1 Homo sapiens cDNA clone 79717 3' similar to gb:X02902 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR-1(DW14) BETA (HUMAN);
6	601	U15085	Human HLA-DMB mRNA, complete cds

G25

1	18	Human mRNA for KIAA0101 gene, complete cds
2	22	Human mRNA for KIAA0035 gene, partial cds
3	23	Human mRNA for KIAA0112 gene, partial cds
4	50	ym09g08.s1 Homo sapiens cDNA clone 47326 3'
5	67	ym49h08.s1 Homo sapiens cDNA clone 51699 3' similar to gb:K02276 MYC PROTO-ONCOGENE PROTEIN (HUMAN);
6	73	yp45f02.s1 Homo sapiens cDNA clone 190395 3'
7	122	yw17d03.s1 Homo sapiens cDNA clone 252485 3'
8	125	ys82e08.s1 Homo sapiens cDNA clone 221318 3' similar to gb:X54942 CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT 2 (HUMAN);
9	126	yv02a07.s1 Homo sapiens cDNA clone 241524 3'
10	153	Human fibroblast growth factor receptor 4 (FGFR4) mRNA, complete cds
11	164	Human thrombospondin 2 (THBS2) mRNA, complete cds
12	177	Homo sapiens transcription factor (CBFB) mRNA, 3' end
13	180	Human matrilysin gene, exon 6 and complete cds
14	181	Human metalloproteinase (HME) mRNA, complete cds
15	185	Human (clone D21-1) L-iditol-2 dehydrogenase gene, exon 9 and complete cds
16	198	Homo sapiens pterin-4a-carbinolamine dehydratase (PCBD) mRNA, complete cds
17	237	Human monocyte-derived neutrophil-activating protein (MONAP) mRNA, complete cds
18	255	Human casein kinase II beta subunit mRNA, complete cds
19	270	Human cytokine (GRO-gamma) mRNA, complete cds
20	281	Human S-adenosylhomocysteine hydrolase (AHCY) mRNA, complete cds
21	301	Human pyrroline 5-carboxylate reductase mRNA, complete cds
22	333	Homo sapiens (E2F-1) pRB-binding protein mRNA, complete cds
23	339	ye87b07.s1 Homo sapiens cDNA clone 124693 3' similar to SP:S40468 S40468 PROTEASOME SUBUNIT RC10-II - ;
24	342	yf18e03.s1 Homo sapiens cDNA clone 127228 3' similar to SP:CH10_BOVIN Q04984 10 KD HEAT SHOCK PROTEIN, MITOCHONDRIAL ;
25	344	yf35a01.s1 Homo sapiens cDNA clone 128808 3' similar to gb:S85655 PROHIBITIN (HUMAN);
26	351	yh73f06.s1 Homo sapiens cDNA clone 135395 3'
27	356	yf53h07.s1 Homo sapiens cDNA clone 26045 3' similar to SP:TF3A_XENLA P03001 TRANSCRIPTION FACTOR IIIA ;
28	378	yg23a06.s1 Homo sapiens cDNA clone 32991 3'
29	382	yg54f12.s1 Homo sapiens cDNA clone 36504 3'
30	393	yj60e02.s1 Homo sapiens cDNA clone 153146 3'
31	412	yh16a01.s1 Homo sapiens cDNA clone 37679 3'
32	447	ym95f04.s1 Homo sapiens cDNA clone 166687 3' similar to gb:X67688 TRANSKETOLASE (HUMAN);
33	476	yb24c06.s1 Homo sapiens cDNA clone 72106 3'
34	487	yb29b04.s1 Homo sapiens cDNA clone 72559 3' similar to gb:M15796 PROLIFERATING CELL NUCLEAR ANTIGEN (HUMAN)
35	488	yb23e03.s1 Homo sapiens cDNA clone 72028 3'
36	518	yb70f06.s1 Homo sapiens cDNA clone 76547 3' similar to gb:X06994 CYTOCHROME C1, HEME PROTEIN PRECURSOR (HUMAN);
37	547	yc17d09.s1 Homo sapiens cDNA clone 80945 3'
38	609	Human chloride channel regulatory protein mRNA, complete cds
39	614	Human 100 kDa coactivator mRNA, complete cds
40	624	Human chromosome segregation gene homolog CAS mRNA, complete cds
41	642	Human mRNA for collagenase (E.C. 3.4.24)
42	654	Human mRNA for snRNP E protein
43	668	Human mRNA for NAD-dependent methylene tetrahydrofolate dehydrogenase cyclohydrolase (EC 1.5.1.15)
44	690	Human gene for melanoma growth stimulatory activity (MGSA)
45	691	H.sapiens ckshs2 mRNA for Cks1 protein homologue
46	692	H.sapiens ckshs2 mRNA for Cks1 protein homologue
47	695	Human humFib mRNA for fibrillarin
48	702	H.sapiens mRNA for IFP53
49	751	H.sapiens PUMP-1 gene encoding PUMP
50	763	Homo sapiens SOX9 mRNA
51	764	H.sapiens mRNA for membrane-type matrix metalloproteinase 1

Figures

Figure 1

S1(G4): clustering 65 tumors using the expression levels of gene cluster G4. A. The boxes in the dendrogram represent clusters; they are colored according to their percentage of ER- tumors (see color bar on left). B. Clusters a,b,c are characterized, respectively, by high, intermediate and low expression levels (see color bar on right).

Figure 2

S1(G10): The boxes in the dendrogram A represent sample clusters that are colored according to the median value of the survival of the patients contained in each cluster, ranging from dark red (median survival of 100 months) to blue (median - 4 months) - see left color bar. B. Clusters a and b exhibits high and low expression levels (see color bar at right), respectively. The central color bar represents p53 status: red - mutant, blue - wt and white - unknown. Members of b are characterized by low expression, low survival and mutant p53.

Figure 3

S1(G33): The boxes in the dendrogram A represent sample clusters that are colored according to the median value of the survival of the patients contained in each cluster, ranging from dark red (median survival of 100 months) to blue (median - 4 months) - see left color bar. B. The clusters a,b, and c exhibit high, intermediate and low expression levels (see color bar at right). The central color bar represents p53 status: red - mutant, blue - wt and white - unknown. Members of a are characterized by high expression, low survival and mutant p53.

Figure 4

S1(G36): A. The genes of G36 gave rise to a very clear partition of the samples to high (cluster a) and low expression levels b. No clinical interpretation of this partition has been found yet.

Figure 5

S(G8): A clear separation of the tumor carcinoma and adenoma samples from the normal samples, using the G8 group of genes. (A) The boxes are colored according to the percentage of the tumor samples. (B) The expression level matrix of S1(G8). Rows correspond to all the samples and the columns correspond to the genes of cluster G8. The matrix shows relatively high expression levels of the G8 genes in the normal samples compared to the tumor samples.

Figure 6

S1(G3): Separation according to protocol A and B. (A) The boxes are colored according to the percentage of protocol A samples, meaning that the red boxes represent protocol A samples and the blue boxes represent protocol B samples. (B) The expression level matrix of S1(G3). Rows correspond to all the samples and the columns correspond to the genes of cluster G3.

Figure 7

S1(G30): Cluster c has fairly high overlap with the blue cluster and contains mainly ER+ tumors. The boxes are colored according to the percentage of ER- tumors.

Figure 8

S1(G25): A clear separation of the tumor carcinoma samples from the normal samples, using the G25 group of genes. (A) The boxes are colored according to the percentage of the tumor samples. (B) The expression level matrix of S1(G25). Rows correspond to all the samples and the columns correspond to the genes of cluster G25. The matrix shows relatively high expression levels of the G25 genes in the tumor samples compared to the normal samples.

Figure 9

S10(G24): A separation within the 18 tumor carcinoma samples on the basis of their expression level over gene cluster G24. (A) Note that cluster b contains the tumor samples 33,34,35,40 and cluster a- the remaining 14 tumor samples. (B) The expression level matrix of S10(G24). Rows correspond to the 18 tumor samples and the columns correspond to the 6 genes of cluster G24. The matrix shows high expression levels of the genes in the tumor samples in cluster b.

Figure 10

S10(G7): A separation within the 18 tumor carcinoma samples on the basis of their expression level over gene cluster G7. (A) Here, the samples 27, 32, 33, 40 are separated from the other tumor samples in cluster a. (B) The expression level matrix of S10(G7). Rows correspond to the 18 tumor samples and the columns correspond to the 7 genes of cluster G7. The matrix shows low expression levels of the G7 genes in the samples which were separated.

Figure 11

S10(G12): A separation within the 18 tumor carcinoma samples on the basis of their expression level over gene cluster G12. (A) Cluster b contains the tumor samples 33, 34, 35, 12, 40 (B) The expression level matrix shows high expression levels of the genes in the tumor samples from cluster b.