Fig. 5
From: The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
Motif enrichment analysis. a STAT1 consensus sequence (TTCNNNGAA) enrichment in peak lists obtained at various tag thresholds. b Comparisons of peak lists derived with ChIP-Peak from data published in [45] versus peak lists published by ENCODE. Here, consensus sequence enrichment serves as a proxy for enrichment in true binding sites. Note that a fair comparison is only possible between peak lists of similar size. c Comparative evaluation of three alternative STAT1 binding motif descriptions: (i) consensus sequence TTCNNNGAA, (ii) PWM from JASPAR and (iii) MEME-ChIP-derived PWM from the peak regions identified by ChIP-Peak (tag threshold 100)