Table 1

Functional signatures of differentially expressed genes induced or suppressed in H-ras-/- and/or N-ras-/- fibroblasts after serum stimulation for 1 hour (G0/G1 transition)

GO ID

Functional category

Gene %

P-value

Relevant genotype

Significant loci


Up-regulated genes

GO:0006955

Immunity and defense

10.5%

0.000209

N-ras-/-

Fas, Cxcl10, Il6, Irf1, Psmb9, Mx1, Mx2, Cxcl2, Tap1, Ifi202b

GO:0006915

Apoptosis

9.6%

0.000250

N-ras-/-

Bax, Bid, Fas, Gadd45b, Perp, Tnfrsf11b, Phlda1, Tnfaip3, Trp53

GO:0003677

Transcription

4.3%

0.000400

N-ras-/-

Rela, Stat1, Stat5a, Trp53

GO:0005515

MAPK signaling cascade

3.2%

0.000896

N-ras-/-

Fas, Mapkapk2, Gadd45b, Dusp8, Trp53, Map3k8, Flnb

GO:0003924

GTPase activity

5.3%

0,002511

N-ras-/-

Ehd1, Mx1, Mx2, Iigp2, Rhoj

GO:0008283

Cell proliferation

10.3%

0.006678

H-ras-/-

Gnb1, Vegfa, Irs2

Down-regulated genes

GO:0007049

Cell cycle

16.7%

0.000109

N-ras-/-

Ccnd2, Ccng2, Cdkn2a, Ppp1cc, Spin, Tsc2, Anapc4, Sash1

GO:0005515

Cell adhesion and cytoskeleton organization

6.3%

0.000244

N-ras-/-

Nras, Pik3r2, Ppp1cc

GO:0004910

Insulin signaling pathway

10.4%

0,000720

N-ras-/-

Nras, Pik3r2, Ppp1cc, Tsc2, Pck2


Specific functional categories assigned by GeneCodis software [66] to particular subsets of the induced or repressed genes included in the dendrograms in Figure 3a. The software tool was used to search for gene annotation co-occurrences in the Gene Ontology (GO) and KEGG pathways databases, assigning values of statistical significance in each case. Functional categories are listed according to increasing P-value of significance for each relevant genotype. Columns provide information on functional GO ID and denomination, percentage of total number of induced or repressed genes in Figure 3a, statistical significance (P-value) of the functional assignment made in each case, and a representative list of differentially expressed loci associated with each functional category.

Castellano et al. Genome Biology 2009 10:R123   doi:10.1186/gb-2009-10-11-r123

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