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. Author manuscript; available in PMC: 2012 Nov 17.
Published in final edited form as: Nature. 2012 Apr 11;485(7398):376–380. doi: 10.1038/nature11082

Figure 1. Topological Domains in the Mouse ES cell Genome.

Figure 1

a, Normalized Hi-C interaction frequencies displayed as a 2D heatmap overlayed on ChIP-Seq data (from ref. 3), DI, HMM Bias State Calls, and domains. For both DI and HMM State calls, downstream bias (red) and upstream bias (green) are indicated. b, Schematic illustrating topological domains and resulting directional bias. c, Distribution of the DI (absolute value, in blue) compared to random (red). d, Mean interaction frequencies at all genomic distances between 40kb to 2Mb. Above 40kb, the intra-versus inter-domain interaction frequencies are significantly different (p < 0.005, Wilcoxan test). e, Box plot of all interaction frequencies at 80kb distance. Intra-domain interactions are enriched for high-frequency interactions. f–i, Diagram of “Intra-domain” (f) and “Inter-domain” FISH probes (g) and the genomic distance between pairs (h). i, Bar chart of the squared interprobe distance (from ref. 7) FISH probe pairs. Error bars indicate standard error (n = 100 for each probe pair).