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.


Shamir et al. BMC Bioinformatics 2005 6:232   doi:10.1186/1471-2105-6-232

Open Data