Fig. 2

Discovery and analysis of Six1-binding sites in primary myoblasts and myotubes. A Venn diagram showing the overlap between Six1-binding peaks in MB and MT. B Proportion of Six1-binding sites, in MB or MT, that overlap various gene features. In this analysis, promoters are defined as the 2 kb region centered at the transcription start site of genes, and the downstream region is defined as the 300 base pairs immediately following the transcription end sites. C Distribution of Six1-binding sites around transcription start sites of genes, in MB and MT. D Results from de novo motif finding using MEME. Redundant motifs and those with lower MEME scores were removed. For each new motif, the most similar motif from the JASPAR database is shown. The enrichment of each motif, in the indicated set of binding site sequences, was calculated. %TP and %FP represent the true positive and false positive percentages, respectively. The Bonferroni-adjusted p value is given under “adj_p-value.” E Biological process GO term enrichment among genes bound by Six1 (all genes within 50 kb of a site bound in MB or bound in MT). Selected terms are shown. N, number of Six1-bound genes with a given annotation; FDR, false discovery rate. The total number of genes assigned to the Six1 peaks is indicated at the top of the respective columns