Figure 3

Differentially expressed genes of Rasless MEFs showing opposite patterns of expression in both BRAF- and MEK1-rescued MEFs. (A) Venn diagram showing the number of shared differentially expressed genes that were simultaneously detected as upregulated in Rasless MEFs (pair-wise comparison to control MEFs, FDR = 0.01) and as repressed in both BRAF- and MEK1-rescued MEFs (pair-wise comparisons to Rasless MEFs, FDR = 0.01). (B) Venn diagram showing the number of shared differentially expressed genes that were simultaneously detected as repressed in Rasless MEFs (pair-wise comparison to control MEFs, FDR = 0.01) and induced in both BRAF- and MEK1-rescued MEFs (pair-wise comparisons to Rasless MEFs, FDR = 0.01). Diagrams A and B generated using the Venny web-based application as indicated in Methods. Red: transcriptional induction and overexpression. Green: transcriptional repression. (C) Functional enrichment of GO Biological Process categories linked to the list of induced and repressed genes identified in panels A and B. The GeneCodis (Gene Annotation Co-occurrence Discovery) functional annotation tool (http://genecodis.dacya.ucm.es) was used to identify specific gene subsets within the list of 432 differentially expressed induced or repressed genes (691 probesets) (panels 3A and 3B; Additional file 4: Table S4, FDR = 0.01) that shared co-occurrent functional annotations linking them, with high statistical significance, to particular Biological Processes. Green bars: repressed loci. Red bars: induced loci. Complete GeneCodis functional annotation analyses are described in detail in Additional file 5: Table S5. Specific p-values for the most significant components of the two main categories depicted in this graph are as follows: Cell cycle: various cell division steps (p-value 2.20E-65). DNA/RNA processing: DNA replication (p-value 7.49E-35); regulation of DNA dependent transcription (p-value 3.08E-14); RNA splicing (p-value 4.38E-14); RNA processing (p-value 8.88E-13); DNA damage response (p-value 4.90E-29); DNA repair (p-value 9.92E-23).