Fig. 5

Preferential Hox DNA-binding fingerprints. An enrichment score based on k-mer frequency per kb, in selected peak sets versus background sequence, is plotted for 5-mer and 8-mer sequences derived from the Slattery et al. in vitro SELEX-Seq study on Hox protein binding [9]. a Enrichment of a set of Hox monomer binding 5-mers for Ubx (all q-value 1e–2 peaks, Experiment 1), Abd-A (all q-value 1e–2 peaks) and Abd-B (all q-value 1e–2 peaks). Although the Abd-B peaks show higher enrichments, overall the three Hox proteins have very similar 5-mer enrichment profiles. b Comparative 5-mer enrichment analysis between Ubx (all q-value 1e–2 peaks, Experiment 2) and Ubx + Hth (328 peaks specific to Ubx + Hth, using q-value 1e–2 peaks) reveals specific changes in the enrichment profile; in the Ubx + Hth peaks, the TTGAT (dark green) 5-mer containing the core Exd motif ‘TGAT’ [13] is preferentially enriched, and the TTTAT (red) 5-mer containing the core Hox motif ‘TTAT’ is more enriched relative to the TTAAT (dark blue) 5-mer containing the core ‘TAAT’ motif. c Enrichment of a set of Exd-Hox dimer binding 8-mers for Ubx (all q-value 1e–2 peaks, Experiment 2) and Ubx + Hth (highest 1000 peaks specific to Ubx + Hth from the overlap between Ubx + Hth and Ubx alone, using q-value 1e–2 peaks, Experiment 2). The 8-mer fingerprint of Ubx in the presence of Exd and Hth strongly resembles the posterior Hox class fingerprints from the SELEX-Seq study (see Fig. 5d). The TGATTTAT (red) and TGATTTAC (magenta) 8-mers clearly relate the in vivo fingerprint to the in vitro posterior Hox fingerprints. d Strip charts showing the distribution of relative binding affinities for each of the eight Exd-Hox dimers to a set of core Exd-Hox binding 8-mers. Image was reproduced from the SELEX-Seq study [9], with permission from Elsevier