Fig. 2

Analysis of Hox binding motifs. a Motif enrichment analysis on the top 500 binding regions (200 bp regions using binding summit position extended ± 100bp) for each Hox protein. Plot titles indicate binding region set used, and motifs are indicated on the x-axis. Enrichment analysis was performed using PWMEnrich for the Hox motifs in the MotifDb database (see the “Materials and Methods” section for details of the motif sets). Enrichment scores [log₁₀(1/p value)] for individual motifs are indicated (dots) together with the median for each motif set (grey bar). Note the differences in y-axis scales. b Motif enrichment analysis on the same binding region sets as in a using the merged HoxA* (combining scores for the Lab, Pb, Dfd, Scr, Antp, Ubx, Abd-A motifs; grey) and Abd-B (purple) motifs. Boxplot with horizontal line indicating the median, box indicating upper and lower quartiles, and whiskers indicating the highest and lowest values excluding outliers. c Motif enrichment analysis for Hox group peaks separated according to chromatin accessibility, using 500 randomly selected “open” (Kc167 ATAC-Seq q < 1e−2) or “closed” regions