Comparison of Su(Hw), Mod(mdg4)2.2, and Shep ChIP–seq profiles in BG3 cells.

<p>(A) Screenshot of Su(Hw), Mod(mdg4)2.2, and Shep ChIP-seq signals at the <i>dnt</i> neuronal-expressed locus. The large gap in ChIP signal corresponds to a highly repetitive region to which sequence reads could not be aligned with high confidence. (B) Screenshot of the <i>caps</i> neuronal-expressed locus. (C) Classification of Su(Hw), Mod(mdg4)2.2, and Shep ChIP-seq peaks in BG3 cells. Number of sites and percentage of total in parentheses corresponding to TSS, transcription start site; CDS, coding sequence; 5′ UTR, 5′ untranslated region; 3′ UTR, 3′ untranslated region. See methods for classification hierarchy of overlapping categories. (D) Heat map of log₂ enrichment scores for pairwise comparisons of binding sites for Su(Hw), Mod(mdg4)2.2, Shep, and additional data sets. Color scale corresponding to enrichment value is indicated (right). Positive values indicate significant enrichment while negative values indicate significant negative correlation of enrichment. Self-self comparisons are indicated in grey, and pairwise comparisons that are not statistically significant (p>0.001) are indicated in white. Numbers along top of each column indicate the total number of features in each data set, and the number of sites overlapping with Shep are indicated in parentheses. Data from Richter (2011) were derived from larval brains and imaginal discs; all other datasets are derived from BG3 cells. Data from modENCODE are indicated by an asterisk. Full heat map with hierarchical clustering is shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003069#pgen.1003069.s004" target="_blank">Figure S4</a>. (E) Binary heat map of Su(Hw), Mod(mdg4)2.2, and Shep binding sites in BG3 cells ordered by supervised hierarchical clustering. Each row represents a single genomic location, and a mark in a column represents the presence of a particular factor.