Table 1 Published transcriptional profiling data sets reexamined in this study. For each set, the Table gives the abbreviation; dimensionality of the data points investigated after pre-processing of the features assayed in the original study; number, description and abbreviation for samples assigned to a category.

BreastER

Node-negative breast carcinomas, P = 3398 (3,398 cDNA clones) [19]

23 Estrogen receptor α positive (ER⁺)

24 Estrogen receptor α negative (ER-)

http://www.nhgri.nih.gov/DIR/Microarray/ER_data.txt

BreastBRCA

Primary breast tumors, P = 3226 (6,512 cDNA clones) [20]

7 BRCA1 mutation (BRCA1)

8 BRCA2 mutation (BRCA2)

7 Sporadic (Sporadic)

http://www.nhgri.nih.gov/DIR/Microarray/NEJM_Supplement

OvarianBRCA

Primary epithelial ovarian adenocarcinomas; P = 6445 (7,651 cDNA clones) [21]

18 BRCA1 mutation (BRCA1)

16 BRCA2 mutation (BRCA2)

27 Sporadic (Sporadic)

http://jncicancerspectrum.oupjournals.org/cgi/content/full/jnci;94/13/990/DC1

LungStanford

Lung tumors; P = 918 (blanks set to average, 24,000 cDNA clones) [22]

41 Adenocarcinomas (AC)

16 Squamous cell carcinomas (SCC)

http://genome-www.Stanford.edu/lung_cancer/adeno

LungBeer

Lung tissue samples; P = 4966 (4,966 cDNA clones) [23]

10 Non-neoplastic (Normal)

86 Adenocarcinomas (AC)

http://www.nature.com/nm/journal/v8/n8/suppinfo/nm733-S1.html

Cutaneous

Cutaneous melanomas; P = 3613 (the "detected" set, 8,150 cDNA clones) [24]

31 Melanoma biopsies (Melanoma)

7 Tumor cell lines (Cell line)

http://research.nhgri.nih.gov/microarray/Melanoma_Supplement

GIST

Tumors; P = 1987 (1,987 cDNA clones) [25]

13 KIT-mutation positive gastrointestinal stromal tumors (KIT⁺)

6 Spindle cell tumors from locations outside gastrointestinal tract (Spindle)

http://research.nhgri.nih.gov/microarray/gist_data.txt

YeohALL

Pediatric, acute lymphoblastic leukemia bone marrows; P = 4196 (10000 variation filter, 12,625 Affymetrix HG_U95Av2 probes) [26]

43 T-lineage ALL (T)

27 E2A-PBX1 (E2A)

15 BCR-ABL (BCR)

79 TEL-AML1 (TEL)

20 MLL (MLL)

64 Hyperdiploid>50 (Hyperdip50)

http://www.stjuderesearch.org/data/ALL1

Prostate

Prostate tissue samples; P = 3958 (12,626 Affymetrix U95a probes) [27]

25 Primary cancer tissue (Tumor)

9 Non-neoplastic tissue (Normal)

http://carrier.gnf.org/welsh/prostate/

Liver

Liver Cancer (Hepatocellular carcinoma); P = 6605 (cDNA clones) [1]

105 Tumor (Tumor)

76 Normal (Normal)

http://genome-www.stanford.edu/hcc/