Fig. 4
From: Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
Modified versus unmodified motifs, combining score and cluster information, for selected transcription factors. These plots come from non–spike-in calibrated data, for the \({500\,\text {bp}}\) regions surrounding peak summits. We clip scores beyond \(\pm 4000\) and plot them at the threshold to maximize dynamic range where most scores occur. Some combinations of the displayed hypothesis pairs had multiple data points (for example, multiple identical hypothesis pairs, but for different data sub-types or stringencies). We aggregated these data points by plotting the maximum score. Below each plot is an asymmetric, diverging, colour scale that further highlights modification-preferring motifs. The colour scales are identical across plots. We depict a larger selection of transcription factors in Additional file 1: Fig. S7. A FEZF2 and C/EBPβ. B Individual motifs illustrating the range of preferences found for C/EBPβ in K562. Left: the least modified-preferring motif (\(\text {score} = -2177.28\)); centre: a motif lacking substantial preference (\(\text {score} = 2.36\)); right: the most modified-preferring motif (\(\text {score} = 3785.86\)). C JUND and JUN. D USF1 and USF2. E c-Myc. F ZFP57. G OCT4. H Individual motifs illustrating the range of preferences found for OCT4. Left: the least modified-preferring motif (\(\text {score} = -762.53\)); centre: a motif lacking substantial preference (\(\text {score} = 2.22\)); right: the most modified-preferring motif (\(\text {score} = 518.01\)). I The most highly significant and centrally enriched DREME motif, for OCT4 hmC-Seal CUT&RUN in mESCs (replicate 1). See Tables 1 and 3 for an overview of modified base notation