Table 2

Functional signatures of differentially expressed genes induced or suppressed in H-ras^-/- and/or N-ras^-/- fibroblasts after serum stimulation for 8 hours (G1 progression)

GO ID

Functional category

Gene %

P-value

Relevant genotype

Significant loci

Up-regulated genes

GO:0003723

RNA binding

15.9%

0,000055

H-ras^-/-

Eif2s1, Rnu3ip2, Nola2, Cpsf4, Rnpc1, Mrpl20, Ddx18, Sf3a1, Hnrpll, Lsm8

GO:0006412

Protein biosynthesis

11.1%

0,000405

H-ras^-/-

Iars, Tars, Eif2s1, Eftud2, Nola2, Rpp30, Mrpl20

GO:0030529

Ribonucleoprotein complex

9.5%

0,001480

H-ras^-/-

Eftud2, Rnu3ip2, Nola2, Mrpl20, Hnrpll, Lsm8

GO:0000398

mRNA splicing

6.3%

0,002982

H-ras^-/-

Rnps1, Eftud2, Sf3a1, Lsm8

GO:0003743

Translation initiation factor activity

4.8%

0,007354

H-ras^-/-

Eif2s1, Eif4ebp1, AU014645

GO:0000074

Regulation of cell cycle

4.8%

0,045790

H-ras^-/-

Ccnd2, Junb, Kras

GO:0005578

Extracellular matrix interaction

9.8%

0,000006

N-ras^-/-

Col18a1, Mmp10, Mmp13, Mmp9

GO:0005634

Cell cycle

14.6%

0,000057

N-ras^-/-

Ccne2, Mcm5, Rbl1, Trp53, Cdc6

GO:0006260

DNA replication

12,2%

0,000035

N-ras^-/-

Mcm5, Pold1, Rrm2, Myst2, Cdc6

GO:0006915

Apoptosis

12.2%

0,002126

N-ras^-/-

Birc5, Bcap29, Perp, Tnfrsf11b, Trp53

Down-regulated genes

GO:0003677

Transcription

21.4%

0,003721

N-ras^-/-

Ankrd1, Meis1, Tcf20

Specific functional categories assigned by GeneCodis software [66] to particular subsets of the induced or repressed genes included in the dendrogram in Figure 3b. 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 3b, 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