Fig. 3

Prediction of differentially bound CTCF peaks using JAMS. A Schematic representation of identifying differentially bound peaks based on the combination of pulldown and control signal in two cell lines. See Methods for details. B Volcano plot showing differential binding of ChIP-seq peaks between GM12878 and HeLa-S3. Significant peaks at FDR < 0.1 are shown in red. C Left: Scatter plot of JAMS-predicted changes in CTCF binding and observed differential binding between GM12878 and HeLa-S3 cells. Peaks with observed log-fc SEM < 0.2). E Predicting differential CTCF binding for peaks with no change in accessibility. Peaks were ranked by accessibility, and the correlation between predicted and observed log-fc of CTCF binding was calculated for sliding windows of 500 peaks (bottom). The average accessibility for each sliding window is shown on top