Figure 2

The MyoD binding regions are largely shared between overexpressed MyoD in MEFs and endogenous MyoD. (A) Overlap of lenti-MyoD peaks with endogenous MyoD peaks. To assess the concordance between the two samples, we selected the top 5K to 110K peaks in each sample based on p-value. We calculated the number of overlapping peaks for the top peak sets at various rank cutoffs in both samples and divided this number by the size of the smaller peak set. Specifically, for a cell corresponding to the top x peaks in sample 1 compared to the top y peaks in sample 2, the fraction is computed as the number of overlapping peaks divided by the smaller value of x or y. (B) The overlapping fractions were calculated as in A and are plotted with color-coding as specified in the figure. For example, in the cell at the row labeled 5K and column labeled 10K, we plotted the fraction of the top 5K peaks in lenti-MyoD that overlap with the top 10K peaks in primary + C2C12 myotubes.