Figure 4

Cell specificity of transcription factor binding motifs associated with STATs. (A) Distinct sets of specific TFBSs were identified in six representative cell types (Figure 2) within +/− 75 bp of the STAT binding peak centers using the MEME-ChIP de novo motif identification program [35]. Top three motifs are shown. The statistical significance of the motifs was estimated using E-value (red) and motif occurrence (black) as described previously [35]. The blue and red dashed boxes indicate the identified GAS motifs and cell-type specific TF binding motifs, respectively. (B) All motif occurrences on the intermediate-confidence STAT binding sites (+/− 75 bp of the peak center) were calculated using the MOODS algorithm with 130 position-frequency matrices available on the JASPAR website (p value <  0.001). The x-axis and y-axis indicate the mean average of normalized motif enrichment scores and motif-covered sites, respectively. Each dot represents a single TFBS and red dots show significantly associated co-TFs (normalized proportion > 0.2 and average of normalized motif enrichment score > 1.5). Red letters indicate TFBSs unique to the given cell-type.