Web Table 4
Hierarchical Clustering	SVD (eigengene 2)				SAM (GIST)
GIST cluster panel c, figure 3
(Listed as appears in gene cluster - see web figure 6 for hierarchical relationship)	Projection	Rank order projection	Correlation	Rank order correlation	Score(d)	Numerator(r)	Denominator(s+s0)	Rank order
SPRY1 sprouty (Drosophila) homolog 1 (antagonist of FGF signaling) Hs.88044	-5.2211	168	-0.4737	468	3.029284467	2.877141944	0.949776086	40
EXTL3 exostoses (multiple)-like 3 Hs.9018	-1.773	1308	-0.3206	1039	1.552046871	1.210679444	0.780053404	386
Homo sapiens cDNA FLJ20848 fis, clone ADKA01732 Hs.325825	-1.4999	1492	-0.2046	1596	1.775291285	1.533454444	0.863776247	281
Homo sapiens cDNA FLJ20848 fis, clone ADKA01732 Hs.325825	-1.7416	1342	-0.1982	1632	2.128176789	1.935148247	0.909298634	170
HSPA8 heat shock 70kD protein 8 Hs.180414	-1.1611	1753	-0.2152	1540	1.414560606	1.1074225	0.782873845	478
SLC4A4 solute carrier family 4, sodium bicarbonate cotransporter, member 4 Hs.5462	-8.1948	33	-0.6492	126	2.865987045	2.96130363	1.033257856	54
TTC1 tetratricopeptide repeat domain 1 Hs.7733	-6.7213	65	-0.7007	78	3.007275211	2.622198333	0.871951567	41
ESTs Hs.25144	-4.8169	216	-0.637	138	2.31533427	1.921638333	0.829961513	120
**ESTs Hs.46564	-4.7827	222	-0.5723	241	2.552613927	2.151425889	0.842832465	87
ESTs Hs.18672	-3.5826	492	-0.6045	185	2.188077954	1.630432901	0.745143882	151
ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 Hs.205353	-4.2327	325	-0.6274	153	2.044795712	1.650828302	0.807331653	193
Homo sapiens cDNA FLJ12141 fis, clone MAMMA1000348 Hs.7514	-4.9363	197	-0.7157	61	1.94438841	1.59360966	0.819594301	222
ESTs Hs.145053	-5.053	183	-0.7208	58	2.292927024	1.834613765	0.800118689	125
PMM1 phosphomannomutase 1 Hs.75835	-3.7885	429	-0.7138	65	1.769273572	1.323863889	0.748252791	287
DNAJB12 DnaJ (Hsp40) homolog, subfamily B, member 12 Hs.7960	-3.7324	448	-0.6369	139	1.804618812	1.403626111	0.777796453	269
ESTs Hs.290825	-9.5864	18	-0.76	29	2.850981977	2.891363673	1.014164136	55
CEP2 Cdc42 effector protein 2 Hs.12289	-6.0351	101	-0.6261	155	2.828404099	2.525825	0.893021263	57
CEP2 Cdc42 effector protein 2 Hs.12289	-6.3512	84	-0.6813	94	2.76141275	2.421284185	0.87682806	63
Homo sapiens mRNA; cDNA DKFZp762M127 (from clone DKFZp762M127) Hs.22483	-4.6282	241	-0.6599	115	2.244557041	1.807473333	0.805269503	135
Homo sapiens WWp2-like mRNA complete cds Hs.333382	-5.6274	137	-0.5578	265	2.872560392	2.629482778	0.915379459	52
ESTs Hs.9094	-9.5228	19	-0.6844	89	3.753180497	3.782223789	1.007738315	20
GUCY1A3 guanylate cyclase 1, soluble, alpha 3 Hs.75295	-8.826	26	-0.5948	201	3.324363242	3.67341	1.104996576	31
GUCY1A3 **guanylate cyclase 1, soluble, alpha 3 Hs.75295	-9.7795	15	-0.6513	125	3.618511962	3.954415556	1.092829206	25
ESTs Hs.22247	-11.033	7	-0.7266	53	3.845043367	4.093676235	1.064663215	15
FLJ20898 hypothetical protein FLJ20898 Hs.25549	-5.737	122	-0.5803	230	2.870689819	2.572611667	0.896164974	53
PRKAR2B protein kinase, cAMP-dependent, regulatory, type II, beta Hs.77439	-4.9423	196	-0.4648	486	3.157508378	2.884961111	0.913682805	38
CUL5 cullin 5 Hs.101299	-2.717	796	-0.4253	624	2.198284362	1.695891728	0.771461489	146
CUL5 cullin 5 Hs.101299	-2.0939	1118	-0.3593	886	1.912870517	1.464312833	0.765505464	226
KIAA0952 KIAA0952 protein Hs.7935	-2.7952	770	-0.2963	1145	2.489776708	2.284232778	0.917444834	96
MYO6 **myosin VI Hs.22564	-2.7011	808	-0.3732	826	2.103424647	1.747878889	0.830968151	178
MYO6 myosin VI Hs.22564	-3.9238	392	-0.3945	736	2.651718428	2.461366944	0.928215801	79
FLJ11149 hypothetical protein FLJ11149 Hs.37558	-3.0101	680	-0.5589	260	1.945649714	1.422544611	0.731141171	221
KDELR2 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2 Hs.118778	-5.3316	155	-0.6597	116	2.686741855	2.209509506	0.822375064	75
LMO2 LIM domain only 2 (rhombotin-like 1) Hs.184585	-6.6644	68	-0.6251	157	2.697591922	2.574071667	0.954210919	73
ABCC4 ATP-binding cassette, sub-family C (CFTR/MRP), member 4 Hs.139336	-5.9614	107	-0.5953	200	2.78496503	2.560810031	0.919512455	60
GG2-1 TNF-induced protein Hs.17839	-7.2016	48	-0.7668	25	2.961692373	2.572487778	0.868587096	44
STK17A serine/threonine kinase 17a (apoptosis-inducing) Hs.9075	-6.638	70	-0.7242	56	2.56133594	2.294821667	0.895947162	85
MGC11257 hypothetical protein MGC11257 Hs.334368	-3.6894	460	-0.5867	216	1.715073341	1.384350764	0.807167094	307
THG-1 TSC-22-like Hs.102447	-4.5637	255	-0.6669	107	2.495415728	1.8938695	0.758939474	95
THG-1 TSC-22-like Hs.102447	-4.9941	189	-0.7174	59	2.240670094	1.774562431	0.791978451	138
CSTF1 cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kD Hs.172865	-4.5478	258	-0.4863	438	3.347593384	2.766113889	0.826299246	29
NUDT4 nudix (nucleoside diphosphate linked moiety X)-type motif 4 Hs.92381	-3.8906	402	-0.56	257	2.485841233	1.92924321	0.77609269	97
FLJ14054 hypothetical protein FLJ14054 Hs.13528	-9.0254	23	-0.5811	227	3.973809757	4.278678889	1.076719609	11
MGAT4A mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A Hs.177576	-6.2205	90	-0.8039	11	2.712487721	2.160495531	0.796499654	70
MGAT4A mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A Hs.177576	-6.0388	99	-0.8074	9	2.333791634	1.904214643	0.815931729	115
CTSL cathepsin L Hs.78056	-9.6895	16	-0.8198	7	3.322875005	3.188869722	0.959671886	32
NEK6 NIMA (never in mitosis gene a)-related kinase 6 Hs.9625	-4.6373	240	-0.6081	181	2.125824663	1.807762253	0.850381635	171
MAGEA10 melanoma antigen, family A, 10 Hs.18048	-3.7553	441	-0.6615	112	1.984198516	1.490168889	0.751018044	211
PCAF p300/CBP-associated factor Hs.199061	-6.8348	61	-0.7683	24	2.580154283	2.256867389	0.874702495	84
KIAA0353 KIAA0353 protein Hs.10587	-11.6078	4	-0.7134	66	3.97846006	4.387667269	1.102855678	10
FLJ20004 **hypothetical protein FLJ20004 Hs.17311	-5.6154	138	-0.6235	159	2.601361273	2.278207778	0.875775234	83
FKBP8 **FK506-binding protein 8 (38kD) Hs.173464	-4.6108	244	-0.7715	21	1.963870543	1.512340321	0.770081473	215
FLJ20208 hypothetical protein FLJ20208 Hs.131776	-4.6186	243	-0.7557	33	2.132439058	1.634012708	0.766264669	168
RBPMS RNA-binding protein gene with multiple splicing Hs.80248	-9.6309	17	-0.7748	19	3.076444383	3.133027778	1.018392465	39
ESTs Hs.44841	-3.7791	434	-0.6613	113	2.270833438	1.647356667	0.725441434	129
Homo sapiens cDNA FLJ11177 fis, clone PLACE1007402 Hs.26243	-13.9112	1	-0.8048	10	3.899763294	4.530972531	1.161858346	14
FLJ20898 hypothetical protein FLJ20898 Hs.25549	-8.3926	31	-0.7145	64	3.711166339	3.373423457	0.908992793	22
Homo sapiens cDNA: FLJ22050 fis, clone HEP09454 Hs.173705	-1.9959	1174	-0.3973	729	1.718076157	1.261173889	0.734061691	306
CLN5 ceroid-lipofuscinosis, neuronal 5 Hs.30213	-3.2631	586	-0.6131	174	2.066080038	1.490753889	0.721537337	190
ADH5 alcohol dehydrogenase 5 (class III), chi polypeptide Hs.78989	-3.3398	558	-0.5599	258	2.172873736	1.630677778	0.750470564	155
AMPD3 adenosine monophosphate deaminase (isoform E) Hs.83918	-11.0426	6	-0.7624	28	3.843662211	3.973048333	1.033662199	16
AMPD3 adenosine monophosphate deaminase (isoform E) Hs.83918	-4.7956	218	-0.6923	84	2.26139622	1.808568426	0.799757429	132
ESTs, Moderately similar to I38022 hypothetical protein [H.sapiens] Hs.238797	-5.9317	111	-0.7244	55	2.751335009	2.254387222	0.819379397	65
ESTs, Moderately similar to I38022 hypothetical protein [H.sapiens] Hs.238797	-5.0218	185	-0.7171	60	2.376866848	1.882160988	0.791866397	106
NIFU nitrogen fixation cluster-like Hs.9908	-4.1396	350	-0.7301	50	2.532697781	1.759934444	0.694885295	91
CA2 carbonic anhydrase II Hs.155097	-12.5945	3	-0.74	41	4.971191811	5.109867932	1.027895951	4
PRKCQ protein kinase C, theta Hs.211593	-13.0635	2	-0.7849	14	5.821060741	5.318023002	0.913583149	1
ESTs Hs.3991	-6.2373	87	-0.7562	32	3.295569681	2.499965679	0.758583772	33
FLJ14466 hypothetical protein FLJ14466 Hs.55148	-4.8481	210	-0.6544	121	2.42573207	1.955061265	0.805967522	101
TMEM2 transmembrane protein 2 Hs.160417	-6.1803	94	-0.7518	34	2.511522387	2.131032778	0.848502402	94
CHN2 chimerin (chimaerin) 2 Hs.286055	-5.6437	134	-0.6276	151	2.947312169	2.4959075	0.846841921	46
CD81 CD81 antigen (target of antiproliferative antibody 1) Hs.54457	-4.5803	251	-0.7017	76	2.346457485	1.793145556	0.764192647	112
108962	-5.1136	178	-0.7101	69	2.707084995	2.074546667	0.766339687	71
SE57-1 CTCL tumor antigen se57-1 Hs.30315	-8.864	25	-0.6949	83	3.904462483	3.634148403	0.930767915	13
FLJ10261 hypothetical protein FLJ10261 Hs.26176	-7.9389	39	-0.4429	553	4.260083643	4.902848333	1.150880768	6
PDE1A **phosphodiesterase 1A, calmodulin-dependent Hs.41717	-3.6077	487	-0.5533	279	2.364269984	1.802711597	0.762481277	108
PROML1 prominin (mouse)-like 1 Hs.112360	-5.7604	120	-0.5606	254	3.936381515	3.204291667	0.81401959	12
Homo sapiens clone 24421 mRNA sequence Hs.10684	-6.6333	71	-0.4284	608	4.303026608	4.436712153	1.031067794	5
**ESTs, Moderately similar to I54375 gene NF2 protein [H.sapiens] Hs.136398	-5.7273	126	-0.4547	514	3.615559652	3.450077401	0.95423053	26
KIAA1492 KIAA1492 protein Hs.91625	-9.9574	13	-0.6355	140	5.448332683	4.96473321	0.911238997	3
ESTs Hs.49776	-11.3734	5	-0.632	146	5.680857192	5.609222963	0.987390243	2
ESTs, Hs.13702	-6.394	83	-0.7146	63	3.44925225	2.730875333	0.791729667	27
**ESTs,  Hs.13702	-6.9915	53	-0.7064	71	3.835456227	3.08069858	0.80321568	17
SLC12A2 **solute carrier family 12, member 2 Hs.110736	-5.958	108	-0.5842	218	3.814663732	3.138963889	0.822867783	19
KIAA0229 KIAA0229 protein Hs.20060	-5.955	109	-0.6232	161	3.750965872	2.981031111	0.794736933	21
KIT v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog Hs.81665	-7.7164	41	-0.5996	194	4.127845389	3.714201778	0.899791884	9
Homo sapiens mRNA; cDNA DKFZp547G133 (from clone DKFZp547G133) Hs.303172	-4.7894	219	-0.5038	395	3.224594571	2.731975	0.84723054	34
SPRY4 sprouty (Drosophila) homolog 4 Hs.285814	-5.9491	110	-0.4918	427	4.171412012	3.687083333	0.883893349	8
INPP5A inositol polyphosphate-5-phosphatase, 40kD Hs.124029	-3.3987	541	-0.5212	348	2.512154537	1.884601667	0.750193365	92
PTP4A3 protein tyrosine phosphatase type IVA, member 3 Hs.43666	-7.3935	46	-0.5576	267	4.211583793	3.946225	0.936993111	7
PTP4A3 **protein tyrosine phosphatase type IVA, member 3 Hs.43666	-6.8079	62	-0.5811	228	3.828236735	3.440138333	0.898622152	18
FUS1 lung cancer candidate Hs.8186	-2.8345	753	-0.5501	287	1.956978448	1.413289444	0.722179361	218
ESTs, Weakly similar to T46371 hypothetical protein DKFZp434P1018.1 [H.sapiens] Hs.23438	-3.9424	388	-0.5301	328	2.71854462	2.129367778	0.783274905	67
**ESTs, Moderately similar to T46371 hypothetical protein DKFZp434P1018.1 [H.sapiens] Hs.118913	-4.1945	335	-0.5658	250	2.64360147	2.087150864	0.789510404	80
CETN2 centrin, EF-hand protein, 2 Hs.82794	-2.5116	893	-0.4096	673	2.106462937	1.613350432	0.76590497	177
HYA22 HYA22 protein Hs.147189	-4.6575	239	-0.7082	70	2.299008086	1.780985556	0.774675638	124
APG-1 heat shock protein (hsp110 family) Hs.71992	-3.3586	551	-0.4245	628	2.424332104	2.020451235	0.833405304	102
Homo sapiens cDNA: FLJ21409 fis, clone COL03924 Hs.172129	-5.6737	130	-0.5131	366	3.676381159	3.215685679	0.874687781	24
APLP2 amyloid beta (A4) precursor-like protein 2 Hs.279518	-5.486	145	-0.6434	131	2.60794139	2.232646111	0.856095202	82
MDS001 x 001 protein Hs.35380	-1.4734	1518	-0.2508	1381	1.570364344	1.252326111	0.797474876	374
**ESTs, Moderately similar to CLC3 HUMAN CHLORIDE CHANNEL PROTEIN 3 [H.sapiens] Hs.171553	-2.0422	1145	-0.3549	908	2.038995881	1.535755247	0.753191932	197
ESTs, Moderately similar to CLC3 HUMAN CHLORIDE CHANNEL PROTEIN 3 [H.sapiens] Hs.171553	-1.7745	1305	-0.3118	1077	1.806623434	1.385288333	0.766783109	267
TCEB1L transcription elongation factor B (SIII), polypeptide 1-like Hs.171626	-2.8337	754	-0.488	435	2.188651826	1.618121667	0.739323472	150
Human DNA sequence from clone RP5-852M4 on chromosome 20  Hs.16475	-1.9124	1219	-0.326	1015	1.990495209	1.516318889	0.761779723	209
DNAJB9 DnaJ (Hsp40) homolog, subfamily B, member 9 Hs.6790	-3.3982	542	-0.5765	234	1.996766858	1.523171111	0.762818706	207
DNAJB9 DnaJ (Hsp40) homolog, subfamily B, member 9 Hs.6790	-2.7953	769	-0.5257	337	1.827085941	1.358873056	0.743737897	260
RAB3A RAB3A, member RAS oncogene family Hs.27744	-2.1784	1063	-0.3618	875	1.683731684	1.342062222	0.797076063	316
Homo sapiens mRNA; cDNA DKFZp564F093 (from clone DKFZp564F093) Hs.18724	-2.7894	771	-0.2626	1314	2.480922803	2.436835	0.982229272	98
PLCB4 phospholipase C, beta 4 Hs.283006	-3.1012	651	-0.4519	527	2.380880321	2.328229438	0.97788596	326
PLCB4 phospholipase C, beta 4 Hs.283006	-3.1053	648	-0.407	684	2.136851879	1.811691597	0.847832091	165
PLCB4 phospholipase C, beta 4 Hs.283006	-4.8234	214	-0.4542	517	2.380880321	2.328229438	0.97788596	105
EPB49 erythrocyte membrane protein band 4.9 (dematin) Hs.274122	-4.8825	205	-0.4451	548	2.781443649	2.688992191	0.966761341	61
Homo sapiens cDNA FLJ14201 fis, clone NT2RP3002955 Hs.193063	-5.2568	162	-0.4293	601	2.688731179	2.81833	1.048200736	74
Homo sapiens cDNA FLJ14201 fis, clone NT2RP3002955 Hs.193063	-6.5673	74	-0.5254	338	2.759070608	2.906431667	1.053409673	64
ESTs Hs.13328	-5.1423	175	-0.441	558	2.771877918	2.791301667	1.007007433	62
DKFZP564O0423 DKFZP564O0423 protein Hs.5028	-5.1578	173	-0.4371	568	2.684779787	2.752399444	1.025186296	76
Homo sapiens cDNA FLJ14201 fis, clone NT2RP3002955 Hs.193063	-5.2366	167	-0.4343	583	2.699885973	2.786557778	1.032102024	72
KIAA1482 KIAA1482 protein Hs.278894	-3.1101	645	-0.4291	603	2.3199536	1.878432556	0.809685399	119
Homo sapiens, Similar to hypothetical protein AB030201, clone MGC:3205, mRNA, complete cds Hs.43621	-3.6579	469	-0.6001	191	2.04442259	1.574938889	0.770358779	195
KIAA1482 KIAA1482 protein Hs.278894	-3.2304	597	-0.5017	401	2.023030412	1.593345833	0.7876035	200
ESTs Hs.23079	-6.835	60	-0.6123	175	3.214786479	2.9930875	0.931037728	36
ABCB1 ATP-binding cassette, sub-family B (MDR/TAP), member 1 Hs.21330	-6.2286	88	-0.5991	195	3.205999863	2.8727875	0.896066008	37
DNCI1 dynein, cytoplasmic, intermediate polypeptide 1 Hs.65248	-3.6093	486	-0.4229	633	2.632769103	2.250049198	0.85463218	81
DNCI1 dynein, cytoplasmic, intermediate polypeptide 1 Hs.65248	-2.8685	737	-0.2875	1186	2.536382137	2.35443713	0.928265932	90
SYNJ1 synaptojanin 1 Hs.127416	-2.6232	840	-0.5296	330	1.773732643	1.278777417	0.720952744	283