Fig. 3

Relationship between unmodified versus modified motif statistical significance of central enrichment (from CentriMo [56]) and modified base calling thresholds across different WGBS and oxWGBS specimens, in mice [51]. We compare each unmodified motif, at each threshold, to its top three most significant modifications for c-Myc and C/EBPβ, but only the single most significant modification for ZFP57. The displayed motif pairs changes at individual thresholds, depending on which motif pairs stay in the top three. See Tables 1 and 3 for an overview of modified base notation. Sign of value indicates preference for the unmodified (negative) motif or the modified (positive) motif. Rows: single ChIP-seq replicates for a particular transcription factor target, one each of A c-Myc (mESCs; Krepelova et al. [57]), B ZFP57 (CB9 mESCs; Strogantsev et al. [23]), and C C/EBPβ (C2C12 cells; ENCFF001XUT). Columns: replicates of WGBS and oxWGBS (mouse CD4⁺ T cells; Kazachenka et al. [51])