Table 1: Summary of the microarray data sets used
Total
Dataset name
1
Description
Array
type2
Probes
Samples
3
4
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(unpublished, GSE443)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(unpublished, GSE474)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)
1
The brief title that is used to refer to the data set in our data base.
2
The array type (Affymetrix GeneChip or two-color spotted microarray).
3
The number of samples (microarrays) in the data set.
4
The total number of probes on the microarray design used.
5
The 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.
6
The number of raw links between the RefSeq genes.
7
In 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.