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. 2014 Oct 7;15(10):482. doi: 10.1186/s13059-014-0482-3

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© Guo et al.; licensee BioMed Central Ltd. 2014

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Comparison of Myc ChIP-Seq occupancy with in vitro binding affinities. (A) The top 30,000 sites occupied by Myc (blue) were rank-ordered and scored by the in vitro occupancy of the best 8-mer in a 100 bp window (y-axis). This was repeated at 30,000 random locations of DNase I-sensitivity (black) and the results were directly compared by ROC analysis (inset). (B) The top 30,000 sites occupied by Myc were rank-ordered by ChIP-Seq signal and scored logarithmically by either normalized ChIP-Seq signal (blue line) or the in vitro occupancy of the best 8-mer in a 100 bp window (black dots). (C) The data in (B) are presented using a default R boxplot (box: 1st to 3rd quartile, line: median, whiskers: 1.5 × interquartile range beyond the box, outliers are stacked) with ChIP-Seq signal in blue and in vitro 8-mers in grey.