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Chunk #106 — Online Methods — 12. DNA Motif Positional Bias in Digital Genomic Footprinting Sites

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Integrative analysis of 111 reference human epigenomes.
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We compute the positional enrichment of each driver motif (Extended Data 9c, Extended Data 10) related to the Digital Genomic Footprinting(DGF) sites in each cell type (Table S5b). For each driver TF motif, we generated two views corresponding to the motif position (the center of the motif instance) relative to the center of closest DGF site (center view) and the motif position relative to the boundary of closest DGF site (boundary view). We only consider the motif instances with closest DGF site within 100bp. For center view, we plotted the motif occurrence density respect to the distance to DGF center for different cell type. For the boundary view, we considered the shortest distance of the center of a motif instance to the both side of DGF boundary, and gave a negative distance value if the motif instance is inside the DGF, otherwise the distance value is positive. Similar to center view, we plot the motif density respect to the derived distance value in the boundary view for each cell type.