Figure 5

Cell-specific combinations of STAT5 binding with other transcription factors in mouse liver and 3T3-L1 cells. (A) Average fold change graphs of nine TF ChIP-seq data sets were superimposed on STAT binding sites of six representative cell-types (Figure 2). The fold change was calculated using the wignorm program which estimates fold change between treatment (ChIPed) value to local bias (control, either IgG or input DNA) [24]. Non-significant graphs were colored grey (bottom). The following data sets were downloaded from the GEO website and processed; GSE17067 – p300, E2F4, CEBPA, FOXA1 and FOXA2 in liver and p300, E2F4 and CEBPA in 3 T3-L1 cells; GSE22078 – HNF4A in liver; GSE27826 – CEBPB, CEBPD and GR in 3 T3-L1 cells. (B) Expression level (RPKM, reads per kilobase of transcript per million mapped reads) of genes in each tissue was measured using the Cufflinks program [45] with an available RNA-seq data set (GSE29278) [46]. The number of genes located near given STAT-associated CRMs (−10 kb ~ TSS ~ +10 kb) is shown (left panel). These genes were defined as STAT-associated. P-value was empirically calculated by the Monte Carlo simulation [47] with 10000 iterations. The same number of tested genes was randomly selected. Bar graph and red rhombus represent expression levels of STAT-associated genes and the P-values in the given cell type, respectively. Asterisk, P-value < 0.1.