Figure 2
Global functional annotation and multiclass comparisons of differentially expressed genes of Rasless MEFs . (A) The GeneCodis functional annotation tool was used to identify subsets of the list of differentially expressed genes of Rasless MEFs (FDR=0.01; Additional file 1: Table S1) sharing co-occurrent functional annotations linking them to specific Biological Processes (Gene Ontology (GO) database; p-values < 0.005), Transcription Factors (TransFac database; p-values < 10-16) or Signaling Pathways (KEGG pathway database; p-values < 10-10). Red: induction. Green: repression. The complete functional annotation analyses are described in Additional file 2: Table S2 and Additional file 3: Table S3. (B) Hierarchical cluster analysis of the absolute expression values of differentially expressed probesets in Additional file 1: Table S1 (FDR = 0.01). Lanes 1–7: Rasless cells. 12-d 4OHT-treated cell lines DU315-6 (1–3, 6, 7) and DU244-1 (4, 5). Lanes 8–21: K-Rasloxcell lines. DU315-6 (8, 9, 11, 13, 14, 20), DU244-1 (17, 21), MCL23-1 (15, 16, 18, 19; puromycin-resistant controls of MEK-rescued lines) and JU10-2 (10, 12; hygromycin-resistant controls for BRAF-rescued lines). Lanes 22–27: BRAF-rescued cell line LG7-6 (22, 23, 26) and MEK1-rescued cell line MCL1-6 (24, 25, 27). Red: overexpression. Blue: repression. Black: unchanged expression. GO categories and associated p-values for horizontal clusters: Clusters 1 and 2: cell-cycle (1.14E-58 and 7.16E-48); cell-division (1.15E-41 and 1.08E-38); mitosis (2.33E-39 and 9.11E-37); DNA replication (6.43E-39 and 2.18E-19). Cluster 1: DNA-dependent transcription (5.1E-26). Cluster 2: chromosome segregation (1.55E-19); DNA damage response (9.06E-19); DNA repair (6.06E-17). Cluster 3: inactivation of MAPK activity (1.91E-04); negative regulation of ERK1/ERK2 cascade (1.79E-03); positive regulation of apoptosis (1.33E-03); negative regulation of cell growth (1.98E-03). Clusters 4 and 6: mRNA processing (1.53E-20 and 1.26E-05); RNA splicing (1.25E-18 and 1.26E-06); transcription, DNA-dependent (9.10E-13 and 1.02E-06). Cluster 7: cellular transport of ions and proteins (5.97E-16); metabolic processes (4.69E-06); small-GTPase-mediated signaling (1.37E-05). Clusters 8 and 9: protein transport (cl.8: 5.99E-09).