The motifs that were predictive of epigenomic modifications70 were compared to Digital Genomic Footprinting data (DGF) in Table S5. This was done in three cell types where both DGF and predictive motifs were available: ‘H1 BMP4 Derived Mesendoderm Cultured Cells’ (E004), ‘H1 BMP4 Derived Trophoblast Cultured Cells’ (E005), and ‘H1 Derived Mesenchymal Stem Cells’ (E006). The motifs that were predictive of the following seven modifications were considered: H3K27me3, H3K27ac, H3K9me3, H3K36me3, H3K4me1, H3K4me3 and DNA methylation valleys (DMV)11. To identify overlaps the predictive motifs were scanned against the modification peaks of the corresponding modification and the location of the best match between motif and sequence was recorded. Then we counted the number of times the locations of the best motif matches overlapped a DGF by at least one bp. These counts were compared to the number of overlaps identified randomly, which was calculated by comparing DGF to random locations within the modifications peaks. The reported random frequency was the average of 100 repeats. To calculate the fold enrichment we divided the observed frequency by the random frequency.
