Figure 6
Reversibility of the microRNA expression profile of Rasless cells and inferred mechanistic implications. (A, B) Overlap of opposing differential miRNA expression profiles between Rasless MEFs and BRAF- and MEK1-rescued MEFs. (A) Venn diagram showing numbers of shared differentially expressed miRNAs (FDR = 0.1) that were simultaneously detected as induced in Rasless MEFs (pair-wise comparison with control MEFs, FDR = 0.1) and as repressed in both BRAF- and MEK1-rescued MEFs (pair-wise comparisons to Rasless MEFs, FDR ≤ 0.19). (B) Venn diagram showing numbers of shared differentially expressed miRNAs that were simultaneously repressed in Rasless MEFs (pair-wise comparison with control MEFs, FDR = 0.1) and induced in BRAF- and MEK1-rescued MEFs (pair-wise comparisons with Rasless MEFs, FDR ≤ 0.19). Red: transcriptional induction. Green: transcriptional repression. Different families and clusters encompassing the 6 upregulated and 34 downregulated miRs identified are highlighted in separate colors. (C) GO Biological Process categories assigned (p-value < 10-4) by the StarBase (sRNA Target Base) functional annotation tool to the panel of 40 differentially expressed miRNAs identified in panels A and B. Bar length quantifies degree of statistical significance for each functional category. (D) Ingenuity Pathways (IPA) software analysis identifying networks of biologically significant functional interactions among the 40 differentially-expressed miRNAs identified in panels A and B and a variety of checkpoint sensors and cell-cycle regulators including Myc, Pten, Rb, Tp53 and Cdkns. Graphic outcome adapted to highlight the most relevant individual miRs or miR families and the key regulators involved in the interactions. mir-17 fam (miR-17, miR-18a, miR-20a, miR-20b, miR-106a, miR-106b, miR-93), mir-27 fam ( miR-27a, miR-27b) and mir-221 fam (miR-221, miR-222) designate those cases where multiple members of the same mir family participate in the indicated regulatory interaction. Green: downregulation; Red: upregulation. Color intensity graded according to d-value of each miRNA entry in Table 1.