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Fig. 6 | Genome Biology

Fig. 6

From: Identification of transcription factor binding sites using ATAC-seq

Fig. 6

Application to ATAC-seq data of dendritic cell (DC) differentiation. a A two-step culture system differentiates ex vivo multipotent progenitors (MPP) to DC progenitors (CDP) and further to classical DC type1 and type2 (cDC1 and cDC2, respectively) or plasmacytoid DC (pDC). b Cell-specific activity of 579 TFs with motifs in either ATAC-seq peaks or footprints by Wellington or HINT-ATAC. Y-axis indicates the difference in activity in cDC1 compared to pDC cells (pDC-cDC1). Names of TFs with significant differential activity values are shown (adjusted p value <0.05; t test) and represent TFs above/below dotted lines. TFs with at least 0.5 log fold change (FC) in gene expression are highlighted (larger fonts), and known DC relevant TFs are marked in green. c Area under the precision recall curve evaluated with Batf3 ChIP-seq in cDC1. d Average cleavage profiles of Tcf4 and Batf3 motifs supported by ATAC-seq peaks, Wellington or HINT-ATAC footprints. e Regions with ATAC-seq and Batf3 ChIP-seq peaks in cDC cells close to DC relevant genes. We display all footprints from Wellington, HINT-ATAC, and all motifs found inside ATAC-seq peaks. While both Wellington and HINT-ATAC find footprints supporting motifs matching summits of Batf3 ChIP-seq peaks (sites 3 and 5 in green), Wellington footprints also support binding sites (2 and 4 in pink), which are not supported by the ChIP-seq signal

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