Fig. 1: In-silico screening using MAmotif.

a Workflow of the in-silico screening. b Top-ranked TF motifs respectively associated with H1 hESC-biased promoter peaks of different histone modifications when compared with K562 cells. c Boxplots displaying the log2-ratios of ChIP-seq intensities between H1 hESCs and K562 cells for promoter peaks of different histone modifications. Peaks were respectively classified by the occurrence of ZNF263, Sox2, and Pou5f1::Sox2 motifs. Each box shows the median (horizontal line), second to third quartiles (box), and Tukey-style whiskers (beyond the box). d–f -Log10 transformed P-values to measure the significance of the association between ZNF263 motif and the H1 hESC-biased promoter peaks of different histone modifications, in comparison to each non-hESC ENCODE cell line. Gray dashed lines correspond to adjusted P-value threshold of 0.05. g Venn diagram showing the overlap between different gene sets. h Enrichment of the overlap between genes that were more highly expressed in H1 hESCs, when compared to each non-hESC ENCODE cell line, and genes occupied by the H3K27ac promoter peaks containing specific TF motifs in H1 hESCs. i P-values to measure the significance of the association between each TF motif and the primed hESC-biased promoter peaks of H3K4me3, when compared to naïve hESCs. j Enrichment of the overlap between genes that were more highly expressed in primed hESCs (primed hESC-high genes), when compared to naïve hESCs, and genes occupied by the H3K4me3 promoter peaks containing specific TF motifs in H1 hESCs. Two independent sets of data are presented. P-values in (b–f) and (i) are reported by MAmotif. Enrichment scores in (g, h) and (j) are defined as the ratio between the number of overlapping genes and that expected by chance, and their P-values are calculated using right-tailed Fisher’s exact test. Exact P-values (d–f, h) are provided in Source Data.