Extended Data Fig. 10: ‘Weavability’ of binding sites is an inherent property of TFs from different DBD classes.
From: Multiple overlapping binding sites determine transcription factor occupancy
(a) Schema to demonstrate the logic of network construction. All incoming and outgoing edges to and from the HOXD13 active 8-mer ‘ACTTTACT’ are shown. Active 8-mers are colored red, inactive 8-mers are colored black. Edges occur between active k-mers only. (b) (left) Network representation of HOXD13 active 8-mers and reverse complements (n = 3,536), connected by directed edges (arrows not shown). 3,446 out of 3,536 nodes (97.5%) form the largest, single connected component. (right) HOXD13 PADIT-seq activity of active 8-mers is plotted against the total number of incoming and outgoing edges per node. The bounds of the box plots define the 25th, 50th and 75th percentiles, and whiskers extend to the furthest data points within 1.5× the interquartile range. * Adjusted P < 0.05, two-sided Wilcoxon tests. (c) (left) Network representation of randomly selected 8-mers and reverse complements (n = 3,536) connected by directed edges (arrows not shown). Only 7 out of 3,536 nodes (0.2%) forms the largest, single connected component. (right) HOXD13 PADIT-seq activity of the 3,536 random 8-mers is plotted against the total number of incoming and outgoing edges per node. (d-h) Network representations and activity distributions for NKX2.5, TBX5, EGR1, Pho4, and Cbf1. For each TF, the fraction of active k-mers in the largest, single connected component is indicated. (i) Among the top 500 uPBM 8-mers and reverse complements, the fraction of nodes in the largest, single connected component is plotted for 200 TFs from 9 different families of DBDs. 1,000 random samplings of 500 8-mers and reverse complements are also shown, and were used to perform the permutation test.
