“Unique” and “redundant” ELK1-bound regions regulate distinct sets of target genes.

<p>(A) K-means clustering of expression levels of genes associated with ELK1-bound regions that show a significant response to siELK1 and/or EGF treatment. Individual clusters (1–8) are separated by dotted lines. (B) Summary profiles of the target genes in clusters 2, 4, 7 and 8. The data are presented as changes of individual (grey) and average (black) expression values of genes in each cluster under each of the four experimental conditions. For each gene, the mean of the signals across all four conditions was set as zero, and expression levels (z-transformed) presented are relative to this value. (C) Distribution of “unique” and “redundant” region-associated ELK1 target genes in the clusters identified in (A), with Chi square or Fisher Exact test-derived P-values. (D) Distribution of genes up- and down-regulated by ELK1 depletion in the “unique” (U) and “redundant” (R) ELK1 target gene datasets after 0 or 30 mins EGF stimulation. (E) Heatmap summary of changes in expression of three genes from the “redundant” ELK1 target dataset upon treatment with siELK1 (from microarrays) or siGABPA (by RT-PCR) (relative to a siGAPDH-transfected control), at 0 and 30 minutes of EGF stimulation. (F) Enrichment of the indicated GO categories in expression clusters identified in (A); P-values were obtained in a Chi-square test and refer to the cumulative enrichment of clusters which cross the dashed line <i>vs.</i> those that do not. (G) Heatmap of the distribution of GO terms identified for “unique” and “redundant” ELK1-associated genes. Each GO term is scored by −log₁₀(P-value). Lines on the left mark terms related to gene expression (grey), actin/migration (green) and cell survival (red).