Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex
Fig 3
Chromatin interactions of gene-pairs in the CIN at 200kb resolution.
(A) Synj1-Dykr1a (yellow nodes) in Chromosome 16 are co-expressed (dashed red link) but their corresponding genomic loci do not interact frequently (no blue link). Both genes have strong chromatin interactions with 4 other genes (grey nodes) resulting a high Jaccard index between them. (B) Kcnc4-Tapan5 (yellow nodes) in Chromosome 3 directly interact (solid blue line) but they are not strongly co-expressed (no dashed red line). This direct chromatin interaction explains the strong co-expression between other gene-pairs in their neighbourhood, such as Wdr47-Tapan5 and Wdr47-Rap1gds1, which are not directly connected in the CIN themselves (no solid blue line). The betweenness centrality measure of the link between Kcnc4-Tapan5 can describe the strong co-expression between their neighbouring genes. Chromatin interaction and co-expression are shown by solid blue and dashed red links, respectively.