Extended Data Fig. 9: Analysis of negative motifs.

a) Footprints at ChromBPNet-derived motif instances for select motifs. Motif instances were separated into four quartiles based on the Fi-NeMo hit correlation score, and footprinting performed separately for each. For each motif, footprinting was for the cell type with the most instances of the motif. Enrichment values represent insertion counts at each position within 500 bp windows around the center of each motif instance, divided by the mean insertion count in the outer 10% at each flank. b-d) Pairwise Jaccard indices were computed to quantify overlap in genomic regions between cell types. b) Pairwise comparisons of overlap in ChromBPNet training peaks, grouped by genomic feature annotation. The cell type pairs with the highest Jaccard indices correspond to different cardiomyocyte clusters. c) Pairwise comparisons of overlap in predictive motif instances, grouped by motif, for a select set of motifs. d) Pairwise comparisons of overlap in motif instances for the positive NFY motif with motif instances of the negative NFY motif in other cell types, and similarly for YY1/2. e) Summary of in silico ablations of motif instances in genomic regions. 1,000 regions per motif were tested, and y-axis represents the difference in predicted log counts between ablated and reference sequences, for one cell type (Heart_c3, fibroblasts), averaged over five folds. f) Number of unique eQTL variant-gene pairs examined per organ. g) Motifs significantly enriched in eQTL variants. Numbers state the total number of variants within all instances of the respective motif across all organs, with the total number of unique gene-variant pairs in parentheses.