Fig. 3: Gene activity at anchor points distinguishes differential contacts.
From: Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C
a, Schematic for detecting feature pair enrichments in GAM- or Hi-C-specific contacts (red and blue, respectively). Each contact is defined by two genomic anchor points that we categorized as either positive or negative for peaks of the respective feature (1). We assessed 105 feature pairs (2) and quantified feature occurrences at the anchor points, filtering out contacts with no feature pairs (3) to identify most distinctive feature combinations between GAM-specific and Hi-C-specific contacts (4). TF, transcription factor. b, Top: frequency of feature pairs in annotated GAM-specific and Hi-C-specific contacts ranked by their presence in the genome. Bottom: heatmap track for the Gini impurity score using the random forest classification, which was trained to discriminate GAM-specific and Hi-C-specific contacts. c, Feature pairs with the highest discriminatory power. Top 10 by mean decrease of Gini impurity, all amplified in GAM (top) and the top 3 feature pairs with the strongest amplification (highest abundance in Hi-C relative to GAM; below dashed line) relative to the abundance of the feature pair in the contact sets. d, Top: contact matrices of GAM-specific and Hi-C-specific contacts at an example locus (chr. 11: 85–95 Mb). Bottom: locations of distinctive features. e, UpSet plots quantifying the co-occurrence of enriched feature pairs selected in c for contacts of each subgroup.
