Table 1.

Major biclusters identified in the test case analysis of the human stress data set.

Bicluster number	Num of Conditions	Num of Genes	Enriched GO (GOid, p-val)	Enriched TF binding site signatures (TRANSFAC id, p-val)	Comments
106	9	79	DNA Replication (GO:0006260, 5.3 × 10-9)	E2F (M00918, 1.3 × 10-7)	Down-regulation of DNA replication genes in fibroblasts exposed to DDT or Menadione.
40	33	74	Mitosis (GO:0007067, 9.3 × 10-19)	NF-Y (M00287, 6.7 × 10-22) IRF-7 (M00453, 9.5 × 10-5)	Down-regulation of mitotic genes in response to various stresses.
104	41	13	Mitosis (GO:0007067, 3.3 × 10-10)	NF-Y (M00287, 3.4 × 10-9)	Down-regulation of mitotic genes in response to various stresses.
16	5	89	Carboxylic acid metabolism (GO:0019752, 3.4 × 10-8)	---	Genes activated in Hela cells in response to Tunicamycin and Menadione
1	6	145	Response to unfolded protein (GO:0006986, 1.2 × 10-7)	---	Genes activated in Hela cells in response to heat shock
9	7	142	Response to unfolded protein (GO:0006986, 7.3 × 10-9)	AP-2alpha (M00469, 5.6 × 10-4)	Genes activated in K562 cells in response to heat shock
111	10	24	Response to unfolded protein (GO:0006986, 1.5 × 10-7)	---	Genes that are activated by heat shock but repressed by crowding in Hela cells
24	6	105	Transcription corepressor (GO:0003714, 1.5 × 10-6)	HIF-1 (M00797, 6.9 × 10-4)	Genes activated in fibroblasts in response to DDT
27	8	200	---	----	Genes activated in fibroblasts in response to oxidative stress (H2O2)
61	9	134	---	----	Genes that are repressed by crowding in fibroblasts.
53	22	51	----	N-Myc(M00055, 2.7 × 10-6)	Genes that are repressed in both Hela cells and fibroblasts.
89	9	115	---	AP-4 (M00005, 2.1 × 10-4)	Genes repressed in Hela cells in response to various stresses.
123	10	31	---	NFkB (M00051, 7.1 × 10-4)	Genes activated in Hela cells in response to DDT.