Locus pairs with high-confidence contacts lie within the same topological domain and have similar replication times. (A) Ratio of the number of significant contacts within topological domain boundaries (intra-domain) to the number of contacts across domain boundaries (inter-domain) at varying FDR thresholds for four different cell lines from Dixon et al. (2012). The black line represents the average of this ratio for the shuffled domains (null model) over all four cell lines. (B) Ratio defined in A for Hi-C data from Lieberman-Aiden et al. (2009) for which no topological domains were defined. We use domain annotations for two human cell lines from Dixon et al. (2012) to compute this ratio for three libraries of Lieberman-Aiden et al. (2009) on two different cell lines at FDR 0.1%. Each legend labeled with a star represents the ratio for the null model (shuffled domains) corresponding to that library. (C) Mean and standard errors of the absolute difference between replication timing values for pairs of loci (rti, rtj) that have a contact at FDR 1% for hESC (Hiratani et al. 2008). We plot the means and standard errors for the distributions of replication timing differences for each 250-kb genomic distance bin up to 5 Mb, for the significant contacts using observed and randomized replication timing (RT) measurements as well as for nonsignificant contacts (FDR >1%) using observed measurements.
