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. 2015 Apr 23;4:e06967. doi: 10.7554/eLife.06967

Figure 4. 8-mer binding profiles of NHR family reveal distinct sequence preferences.

Figure 4.

Left, ClustalW phylogram of nuclear hormone receptor (NHR) DBD amino acid sequences with corresponding motifs. TF labels are shaded according to motif similarity groups identified by PWMclus. Center, heatmap showing E-scores. NHRs are ordered according to the phylogram at left. The 1406 8-mers with E-score > 0.45 for at least one family member on at least one PBM array were ordered using hierarchical agglomerative clustering. Each TF has one row for each of two-replicate PBM experiments (ME or HK array designs). Right; recognition helix (RH) sequences for the corresponding proteins, with identical RH sequence types highlighted by colored asterisks. Variant RH residues are underlined at bottom. Right, matrix indicates cluster membership according to PWMclus. Top and bottom, pullouts show re-clustered data including only the union of the top ten most highly scoring 8-mers (taking the average E-score from the ME and HK arrays) for each of the selected proteins. E-scores for k-mers in all three heatmaps are available in Figure 4—source data 1.

DOI: http://dx.doi.org/10.7554/eLife.06967.014

Figure 4—source data 1. Table showing 8-mer E-score profiles of NHRs analyzed by PBMs.
8-mers bound by at least one NHR with an E-score ≥0.45 for all the C. elegans NHRs that have been analyzed by PBMs (center panel) and a table of pullouts (top and bottom panel) showing average (ME and HK) E-scores of the union of the top ten highly scoring 8-mers bound by at least one NHR within the selected motif cluster.
DOI: http://dx.doi.org/10.7554/eLife.06967.015
elife06967s003.xlsx (1.1MB, xlsx)
DOI: 10.7554/eLife.06967.015