Figure 2

Gene expression analysis of IPC cells exposed to the PKA-activating cAMP analog N⁶-MB-cAMP. IPC_WT or IPC cells stably over-expressing ICER (IPC_ICER) or Bcl2 (IPC_BCL2), were exposed for 2 h to the PKA activator N⁶-MB-cAMP (700 μM). The transcriptome was analyzed by Affymetrix gene array (U230A, 15 866 probe sets). (a) The 82 transcripts increased (red) or decreased (blue) >2-fold in either IPC_WT or IPC_ICER or IPC_BCL2 are shown in a hierarchical clustering diagram. Genes in green have known cAMP responsive elements (CRE) in the promoter region from −3000 to +300 bases from the transcriptional start site. (b and c) The Venn diagram circles show the number and overlap of transcripts upregulated (b) or downregulated (c) >2 fold by N⁶-MB-cAMP in IPC_WT (grey), IPC_ICER (cyan), and IPC_BCL2 (pink) cells. (d) The panel shows that the fold regulation by N⁶-MB-cAMP in IPC_WT cells correlates well (r²=0.866) with that in IPC_BCL2 cells (Δ), but poorly (r²=0.287) with that in the IPC_ICER cells (O). The dotted line represents perfect correlation. Note that only transcripts regulated more than 2-fold are included. (e) Biological processes over-represented among the N⁶-MB-cAMP regulated genes according to the http://www.pantherdb.org tool are shown. Two processes had significantly fewer and seven had more regulated genes than the average. The P-values ranged from 0.003^* (intracellular protein transport) to 0.047 (protein metabolic process). The number of regulated genes for each process is shown above each bar (see Supplementary Table S5 for details)