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. 2018 Feb 7;9:542. doi: 10.1038/s41467-018-03017-1

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© The Author(s) 2018

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — Pan-cancer analysis of strong vs. weak TAD boundaries (high sequencing depth = 80 million intrachromosomal read pairs). a Schematic of pan-cancer analysis (left panel) and classification of focally deleted boundaries in cancer according to their strength (right panel). b Schematic of pan-cancer analysis (left panel) and classification of focally duplicated boundaries in cancer according to their strength (right panel). c Schematic of pan-cancer analysis (left panel) and co-duplications of TAD boundaries with regular enhancers and super-enhancers in cancer (right panel). d Snapshot of the MYC locus: a strong boundary (black bar) is frequently co-duplicated with MYC and potential super-enhancers in cancer patients (highlighted area). IGV tracks from top to bottom: average insulation score across cell types (gray), strong boundaries (black bars), super-enhancer track from SEA (blue bars), RefSeq genes, duplication frequency (red graph) and ICGC patient tandem duplications (red bars). All statistical tests are paired two-sided Wilcoxon rank-sum tests between distributions defined across samples (each sample is a dot in the boxplots). The box in each boxplot represents the first (Q1) and third (Q3) quartiles and the ends of the whiskers are positioned 1.5*(Q3-Q1) away from the ends of the box.