Extended Data Figure 10: Full-resolution view of global pairwise transcription factor co-association matrix.

As outlined in Fig. 2a, the significance of co-binding (co-association strength) 2 kb upstream and 200 bp downstream of TSSs was measured reciprocally between all binding experiments (IntervalStats²⁴, see Methods). For each comparison (N_C = 34,782), the fraction of significant (P < 0.05) co-binding events was computed and the mean fraction of reciprocal tests is reported (N_T = 17,391). Co-association scores are scaled by the standard deviation (uncentred) for visualization purposes. Co-associations were examined among 292,466 binding sites outside of XOT regions. Inset (i) shows the distribution of global transcription factor co-association strengths from pairwise comparisons of 187 ChIP-seq experiments. The distribution of co-association strengths is shown from comparisons of all (distinct) ChIP-seq experiments (N_DE = 17,391, light blue) and from comparisons of ChIP-seq experiments from distinct factors (N_DF = 17,197, dark blue). The 75th, 90th and 95th percentiles from comparisons between distinct factors (CS_75% = 0.2437, CS_90% = 0.3589 and CS_95% = 0.4266) are indicated as light red, red and dark red dashed lines, respectively. Co-association strengths between FOS-1–JUN-1 in L1, L3 and L4 larvae are indicated with arrows. Inset (ii) highlights the similarity (Wilcoxon test, P = 0.4913) between distributions from distinct factors and distinct experiments.