Table 1: Summary of the microarray data sets used
Dataset name1	Description	Array type2	Samples3	Total
Probes4	Refseq
Genes5	Raw links6	Reference7	
alizadeh-lymphoma	lymphoma	two color	96	4022	1759	25746	(Alizadeh et al. 2000)	
allander-gist	GIST sarcoma	two color	19	1987	1205	1251	(Allander et al. 2001)	
armstrong-mll	leukemia	Affymetrix	72	12582	8242	213456	(Armstrong et al. 2002)	
bhattacharjee-lung	lung cancer	Affymetrix	203	12600	8243	243303	(Bhattacharjee et al. 2001)	
bittner-melanoma	melanoma	two color	38	8067	4382	16141	(Bittner et al. 2000)	
bleharsky-leprosy	leprosy	Affymetrix	11	12625	8257	4760	(unpublished, GSE443)	
butte-relevance	NCI-60 tumor cell lines	Affymetrix	68	7240	4906	81755	(Butte et al. 2000)	
chang-fibroblasts	fibroblasts	two color	50	44945	13079	328274	(Chang et al. 2002)	
chaussabel-parasite	parasite response	Affymetrix	28	12625	8243	80559	(Chaussabel et al. 2003)	
chen-liver	liver cancer	two color	207	41027	9169	597313	(Chen et al. 2002)	
cheok-leukemia	leukemia	Affymetrix	120	12600	8243	258731	(Cheok et al. 2003)	
coller-telomerase	breast cancer	Affymetrix	20	5119	4119	19895	(Smith et al. 2003)	
dhanasekaran-prstate	prostate cancer	two color	53	9984	5613	161097	(Dhanasekaran et al. 2001)	
diehn-cd28	T-cells	two color	68	35844	10400	1635022	(Diehn et al. 2002)	
dyrskjot-bldderrecur	bladder tumors	Affymetrix	31	7129	5418	60343	(Dyrskjot et al. 2003)	
dyrskjot-bldderstage	bladder tumors	Affymetrix	40	7129	5418	58461	(Dyrskjot et al. 2003)	
garber-lung	lung cancer	two color	73	23091	9171	258866	(Garber et al. 2001)	
golub-leukemia	leukemia	Affymetrix	72	7129	5418	52283	(Golub et al. 1999)	
greenberg-myopathy	inflammatory myopathy	Affymetrix	12	12600	8243	5280	(Greenberg et al. 2002)	
gruvberger-estrogen	breast cancer	two color	58	3369	2756	24781	(Gruvberger et al. 2001)	
hedenfalk-breast	breast cancer	two color	22	3226	2253	1265	(Hedenfalk et al. 2001)	
hedenfalk-familial	breast cancer	two color	16	4754	3312	673	(Hedenfalk et al. 2003)	
houmard-obesity	obesity	Affymetrix	24	22283	12057	12944	(unpublished, GSE474)	
huang-breast	breast cancer	Affymetrix	89	12558	8257	137512	(Huang et al. 2003)	
huang-papillary	thyroid papillary tumors	Affymetrix	16	12558	8243	9634	(Huang et al. 2001)	
jazaeri-breast	breast cancer	two color	61	6445	3644	46187	(Jazaeri et al. 2002)	
khan-bluecell	blue cell tumors	two color	88	2276	1952	19868	(Khan et al. 2001)	
khatua-astrocytoma	astrocytoma	Affymetrix	13	12625	8257	10072	(Khatua et al. 2003)	
leung-gastric	gastric cancer	two color	126	42915	12657	993195	(Leung et al. 2002)	
luo-prostate	prostate cancer	two color	25	6500	4354	14873	(Luo et al. 2001)	
ma-breast	breast cancer	two color	61	1940	1569	10086	(Ma et al. 2003)	
macdonald-mblastoma	medulloblastoma	Affymetrix	31	2059	1309	3179	(MacDonald et al. 2001)	
nielsen-sarcoma	sarcoma	two color	46	5520	3359	25175	(Nielsen et al. 2002)	
perou-breast	breast cancer	two color	26	5519	3027	42105	(Perou et al. 1999)	
perou-portraits	breast cancer	two color	84	8987	5701	167826	(Perou et al. 2000)	
pomeroy-embryonal	brain tumors	Affymetrix	90	7129	5418	85909	(Pomeroy et al. 2002)	
ramaswamy-cancer	tumor, normal	Affymetrix	255	16063	9528	372500	(Ramaswamy et al. 2001)	
rickman-glioma	glioma	Affymetrix	51	7069	5418	60169	(Rickman et al. 2001)	
rosenwald-leukemia	leukemia	two color	102	17530	3751	129814	(Rosenwald et al. 2001)	
ross-breast	breast cancer	two color	24	39759	12437	3409	(Ross and Perou 2001)	
ross-nci60	NCI-60 tumor cell lines	two color	68	9703	5837	45468	(Ross et al. 2000)	
shipp-dlbcl	lymphoma	Affymetrix	77	7129	5418	87486	(Shipp et al. 2002)	
sibille-pfc	prefrontal cortex	Affymetrix	75	22283	12057	824563	(Erraji-BenChekroun et al.)	
singh-prostate	prostate cancer	Affymetrix	102	12600	8242	248952	(Singh et al. 2002)	
sorlie-breast	breast cancer	two color	85	21832	9132	1578	(Sorlie et al. 2001)	
sorlie-breasttumor	breast cancer	two color	122	46613	13121	14351	(Sorlie et al. 2003)	
spannhake-asthma	asthma	Affymetrix	12	12625	8257	128303	(unpublished, GSE470)	
staunton-nci60	NCI-60 tumor cell lines	Affymetrix	60	7129	5418	51286	(Staunton et al. 2001)	
su-humanmouse	Diverse tissues	Affymetrix	85	12600	8243	241088	(Su et al. 2002)	
tezak-jdm	dermatomyositis	Affymetrix	10	7129	5418	7941	(Tezak et al. 2002)	
vahey-hiv	viral infection	Affymetrix	30	7129	5418	60268	(Vahey et al. 2002)	
vantveer-breast	breast cancer	two color	117	16783	11312	752390	(van 't Veer et al. 2002)	
virtaneva-aml8	leukemia	Affymetrix	21	6086	4804	5923	(Virtaneva et al. 2001)	
welle-muscle	muscle	Affymetrix	12	12533	8243	2670	(Welle et al. 2001)	
welsh-ovarian	ovarian cancer	Affymetrix	49	7129	5418	52459	(Welsh et al. 2001)	
welsh-prostate	prostate cancer	Affymetrix	55	12626	8258	260155	(Welsh et al. 2001)	
west-breast	breast cancer	Affymetrix	49	7129	5418	84842	(West et al. 2001)	
whitfield-cellcycle	cell cycle, tumors	two color	114	45060	12801	1547199	(Whitfield et al. 2002)	
yeoh-leukemia	leukemia	Affymetrix	248	12625	8257	257979	(Yeoh et al. 2002)	
yoon-p53	colorectal cancer	Affymetrix	12	7129	5418	53305	(Yoon et al. 2002)	

1The brief title that is used to refer to the data set in our data base.
2The array type (Affymetrix GeneChip or two-color spotted microarray). 
3The number of samples (microarrays) in the data set. 
4The total number of probes on the microarray design used.
5The number of unique RefSeq genes represented on the array that were included for analysis. This is usually much lower than the number of probes because many probes do not refer to RefSeq genes, and a gene could be represented by more than one probe. For Affymetrix data sets, “probe” refers more precisely to “probe sets” while for spotted microarrays it refers to a spot.
6The number of raw links between the RefSeq genes.
7In three cases where the data is not published, the Gene Expression Omnibus accession number is given. Full details of the data sources are available on our web site.