Fig. 1: Signature confidently maps NHCCs.

a Supervised learning in Signature. Scheme depicts genomic regions between different chromosomes that are evaluated for their significantly interacting (red triangle = positive z scores) and non-interacting bins (blue triangle = negative z scores). All genomic regions are queried against all other regions in an ‘All vs. All’ approach. Right: example of interaction weights with significance cutoffs (dashed lines) between two chromosomes. b Unsupervised learning by Community Detection (CD) in Signature. CD groups clusters of similar properties (i.e., interaction weights of intra-chromosomal interactions and NHCCs) in communities (black, red, blue). c Features of the body map analyzed with Signature. 161 billion (B) mapped reads derived from 62 datasets generated a compendium of 2n genomic interactions across human cell types, separated by sex. d Consecutive bins of each chromosome are strung together to generate the chromosomal outlines and to visualize CD-approximated genome topology across 62 Hi-C datasets. Large chromosomes 1-7 (red & pink) and small, gene-dense chromosomes 16-22 (blue & black) are highlighted. e Acrocentric chromosomes 13-15, 21, and 22 are colored in genome topology map. Telomeric p- arms and q-arms are shown as black squares or asterisks, respectively. Enlargement depicts how CD strung bins together to generate chromosomal outlines. f Ideograms depict reported NHCCs tested by Signature. Each heatmap represents a pair of interacting chromosomes. Mean z-scores are shown and red lines indicate genomic positions of reported loci (shown in Mb = megabases). Enlargements highlight region of interest, each cell is a 1 Mb bin. Unmapped regions such as acrocentric p arm of chromosome 14 are shown in white. g Interaction density per megabase of intra-chromosomal interactions (gray) and NHCCs (red) per chromosome (n = 62 Hi-C datasets). Box limits represent upper and lower quartiles. Central boxplot line represents the median and whiskers represent 1.5x IQR. h Same as panel g but for number of genes per chromosome (n = 62 Hi-C datasets).