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. 2022 Jan 29;15:4. doi: 10.1186/s13072-022-00436-9

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© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 6 — Functional similarity of pairs of genes in autosomal CTCF TADs. Olfactory genes and paralogous gene pairs have been excluded in all panels. A–C Top panel: median GO semantic similarity, number of gene pairs with ≥ 1 shared pathways or number of gene pairs with ≥ 1 shared PPI for pairs of genes vs binned distance in the genome and 1000 random genomes. Bottom panel: stars indicate bins with a significantly higher functional similarity in the genome vs 1000 random genomes (FDR corrected p-value < 0.05). D–F TADs called using both Arrowhead and TopDom; in both ESC and cortical neuron Hi-C. Median p-value: p < 0.001 = ***, p < 0.01 = **, p < 0.05 = *, NS = not significant. A Distribution of MF GO semantic similarity for pairs of genes binned by distance in the genome vs 1000 random genomes. B Distribution of the number of pairs of genes sharing ≥ 1 pathway binned by distance in the genome vs 1000 random genomes. C Distribution of the number of pairs of genes sharing ≥ 1 PPI binned by distance in the genome vs 1000 random genomes. D Median MF GO semantic similarity for pairs of genes in CTCF TADs (dotted line) compared to the distributions of median MF semantic similarity for 100 sets each of: random CTCF TADs and random genome CTCF TADs (Wilcoxon test, median p-value, median ES = effect size calculated using r for Wilcoxon). E Proportion of annotated pairs of genes sharing ≥ 1 pathway in CTCF TADs and the median proportion of pairs of genes sharing ≥ 1 pathway in 100 sets each of: random CTCF TADs and random genome CTCF TADs (Fisher’s exact test, median p-value). F Proportion of annotated pairs of genes sharing ≥ 1 PPI in CTCF TADs and the median proportion of pairs of genes sharing ≥ 1 PPI in 100 sets each of: random CTCF TADs and random genome CTCF TADs (Fisher’s exact test, median p-value)