Extended Data Fig. 9: Higher order chromatin organization and DNA mismatch repair activity.
From: Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure
a, Average profiles of mutation loads across boundaries delineating inactive to active domains MSS and MSI samples from colorectal adenocarcinoma, uterine adenocarcinoma, gastric adenocarcinoma, stomach adenocarcinoma, glioblastoma multiforme (CNS-GBM), pancreas adenocarcinoma and liver cancer; with dashed lines for MSI samples. b, Number of mutations in colorectal adenocarcinoma samples per megabase active versus inactive domains. MSI sample is denoted with cyan color. c, Schematic describes the TAD boundary strength calculation. Briefly, for each TAD boundary we obtained a matrix around 400Kb up- and down-stream of the boundary by centering the TAD boundary in the middle. Next we calculated the log2 ratio of sum of interactions occurring within TADs and between TADs for each boundary region. d, Average TAD boundary strength profiles across all TAD boundaries (n = 2477) in healthy colon tissue and colon cancer cell line Hi-C data. The center line is the median; box limits are the upper and lower quantiles; whiskers represent 1.5x the interquartile range.
