SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
Fig 5
Sequence preferences of GM12878 DNase-seq peaks.
(A) Heatmap showing the group scores for top groups over 16,891 GM12878 DNase-seq peaks. Note that some peaks have a sequence signal for a single factor while others have signals for multiple factors (FDR-corrected p < 0.01). All the group predictions identified by “*” have been validated by ChIP-seq data, while “#” indicates no ChIP-seq data available in ENCODE. The dashed boxes highlight the specific examples illustrated in Fig 5B. (B) The left panel shows a DNase peak with a strong score for a single transcription factor (NRF1). The middle panel shows DNase peaks with moderate scores for both BATF and RUNX. The left panel shows different binding preferences in adjacent split peaks derived from a single broad peak. All the predictions are validated by ChIP-seq.