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. 2013 May 8;41(13):6391–6402. doi: 10.1093/nar/gkt355

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© The Author(s) 2013. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 4. — Motif scores correlate with in vitro binding affinity. (A) The ChIP-seq–derived PU.1 consensus PWM (sequence logo is shown on top) comprises ∼3300 different 12mers. Twenty-five representative 12mers overlapping the PWM are shown below the logo next to their motif log-odds scores. (B) Scatter plot showing scores of motifs relative to the frequency of in vivo binding events across the repeat-masked genome (only motifs with >100 occurrences across the masked genome are included). (C) Scatter plot showing the correlation between microscale thermophoresis-derived dissociation constants (K_D-values) for the interaction between recombinant full-length PU.1 and double-stranded oligonucleotides [including the ones listed in (A)] with corresponding motif log-odds scores. Only K_D-values <1500 mM were plotted. Oligos with larger K_D-values (between 1500 and 4500 mM, 12 in total) had low-log-odds scores (between 6.7 and 7.6). A complete list of K_D- and log-odds score values is given in Supplementary Table S1.