Fig. 5

Pairwise gene co-expression in autosomal CTCF TADs. Olfactory genes and paralogous gene pairs have been excluded in all panels. A–B Top panel: median expression correlation coefficient (spearman) for pairs of genes vs binned distance in the real genome and 1000 random genomes. Bottom panel: stars indicate bins with a significantly higher median expression correlation in the real genome vs 1000 random genomes (FDR corrected p-value < 0.05). Jitter has been applied on the y axis to allow clearer visualisation of close together points. A Expression correlation coefficients were calculated using RNA-seq from two replicates each of ESC, neural progenitor cells (NPC) and cortical neuron cells. B Expression correlation coefficients were generated using mouse ESCs differentiating to primordial germ like cells (PGC) and forebrain RNA-seq from encode. The mouse ESCs differentiating to PGC RNA-seq was generated with three replicates each of ESCs, epiblast like cells (day 2), PGC (day 4) and PGC (day 6). The forebrain RNA-seq was generated with two replicates each, of embryos of varying ages. C–D Median expression correlation coefficient (spearman) for pairs of genes in CTCF TADs (dotted line) and median expression correlation coefficient (spearman) in 100 sets each of: random CTCF TADs and random genome CTCF TADs. CTCF TADs called using both Arrowhead and TopDom, in both ESC and cortical neuron (CN) Hi-C (Wilcoxon test, median p-value: p < 0.001 = ***, p < 0.01 = **, p < 0.05 = *, NS = not significant, median ES = effect size calculated using r for Wilcoxon). C Expression correlation coefficients were calculated using RNA-seq from A. D Expression correlation coefficients were calculated using RNA-seq from B