LOcating Non-Unique matched Tags (LONUT) to Improve the Detection of the Enriched Regions for ChIP-seq Data
Figure 6
An evaluation of the performance of LONUT on ChIP-seq datasets of three TFs from four cell lines.
A. De novo motif discovery on three TFs on four cell lines using the ChIPMotifs identifying the canonical binding motifs for all four data. For NRSF in GM12878 and H1 cells, and YY1 in K562 cells, we identified each canonical motif for both Top 500 CMT peaks and Top 500 Extra peaks. For the TCF7L2 data, we particularly examined it three subsets including top 1/3 peaks, middle 1/3 peaks and bottom 1/3 peaks. We were able to recover a 6-mer TCF7L2 core motif from all sets of peaks. B. A motif recovery plot showing that these 6-mer core motifs (W1) identified by our ChIPMotifs are present in a large percentage of the binding peaks with a gradually percentage reduction along more peaks consideration.