TF transcriptional responses to SCN EGFR activation and their expression correlations with target gene groups. (a) Gene expression responses to EGFR activation of five TFs implicated by the gene group enrichment (qRT-PCR). c-Jun is consistently down-regulated during both day and night, c-Ets1 and Creb1 are both down-regulated during the day and up-regulated during the night, C/EBPα is consistently up-regulated during the night only, and C/EBPβ is consistently down-regulated during the day only. Red and blue shades represent positive and negative changes in expression, respectively. dE.1, dE.2, and dE.3 represent scaled normalized -ΔCt values (approximate log2 expression levels, see Materials and methods) in daytime rats while dE.N1 and dE.N2 represent scaled -ΔCt values in nighttime rats. To facilitate comparisons between genes, expression differences were divided by their maximum absolute values. 2 displays the relative animal-animal variability in the expression responses. (b) Statistically significant (p < 0.01) average absolute Pearson correlations between scaled log2 TF expression levels (qRT-PCR) and scaled log2 expression levels of EGF responsive genes (microarray). Creb1 expression was strongly correlated with expression profiles of putative circadian time dependent target gene groups whereas c-Ets1 expression was more weakly, but nevertheless significantly, correlated with those gene groups. c-Jun was predicted to regulate target genes in a circadian time dependent manner but has a circadian time independent expression response that is significantly correlated with the circadian time independent gene group. C/EBPβ expression was significantly correlated with putative daytime C/EBP target genes while C/EBPα expression was significantly correlated with putative C/EBP target nighttime responsive genes. Black squares indicate the absence of statistically significant correlations whereas orange squares indicate the presence of statistically significant correlations. Correlation strength is represented by color intensity, with the lowest significant average absolute correlation being 0.5 (between C/EBPα and the overall EGF responsive gene set) and the highest significant average absolute correlation being 0.9 (between Creb1 and the genes responsive to EGF during the day and the night). Images for (a) and (b) were created using the free program Treeview .
Zak et al. Genome Biology 2006 7:R48 doi:10.1186/gb-2006-7-6-r48