Fig. 4

Motif enrichment analysis of the DNA sequences underpinning the binding profiles. Motif enrichment analysis was performed using PWMEnrich for the Hox and Hox cofactor PWM motifs in the MotifDb database. Enrichment scores [log₁₀(1/p-value)] for individual motifs are indicated (grey dots) together with median for each motif set (coloured bar). a Comparing motif enrichments for DNase1 (1000 random q-value 1e–2 peaks) and Ubx (1000 q-value 1e–2 peaks with highest Ubx versus DNase1 differential signal; Experiment 1) reveals that DNase1 peaks in general are not enriched for Hox PWMs, whereas Ubx peaks show clear enrichment with the posterior Hox gene PWMs showing the highest enrichment. Little or no enrichment is observed for Hox cofactor PWMs. b Comparing Ubx wild type (1000 q-value 1e−10 peaks with highest Ubx versus DNase1 differential signal; Experiment 2) and Ubx mutant (1000 q-value 1e−10 peaks with highest Ubx mutant versus DNase1 differential signal), reveals lack of Hox and Hox cofactor PWM enrichment in Ubx mutant peaks. c Comparing Ubx (1000 q-value 1e–2 peaks with highest Ubx versus DNase1 differential signal; Experiment 1) and Abd-B (1000 q-value 1e–2 peaks with highest Abd-B versus DNase1 differential signal), demonstrates that Abd-B peaks have markedly higher enrichments for Hox PWMs but otherwise a similar enrichment profile (cf. Ubx in a). d Comparing Ubx (328 random q-value 1e–2 peaks common to Ubx Experiment 2 and Ubx + Hth) and Ubx + Hth (328 q-value 1e–2 peaks specific to Ubx + Hth); in the presence of Exd and Hth, the enrichment of Exd and Hth PWMs in the Ubx peaks is increased and the enrichment of Hox PWMs is shifted towards a greater relative preference for Abd-B motifs