Fig. 5
From: Identification of transcription factor binding sites using ATAC-seq
Competing methods and protocols comparison. a Comparative evaluation of HINT-ATAC, HINT, Wellington, DNase2TF, DeFCoM, and PIQ on the test dataset (H1-ESC and K562 cells). A higher ranking score indicates highest recovery of ChIP-seq supported binding sites. p values are based on the Friedman-Nemenyi test. We only show the significant p values of the top 3 methods (see Additional file 1: Table S23–S24 for complete results). b AUPR values of DNase-seq (DH) vs ATAC-seq (Omni) for 91 factors, of which 41 factors obtain higher AUPR using ATAC-seq. c The footprint profiles of two factors with the highest AUPR difference are shown. d Difference in AUPR of double-hit DNase-seq and Omni ATAC-seq by grouping TFs by transcription factor families as defined in JASPAR database. Only families with more than 10 TFs are shown, and p values are obtained with a t test (mean = 0)