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. 2022 Jun 30;54(7):963–975. doi: 10.1038/s41588-022-01100-4

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© The Author(s) 2022

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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Extended Data Fig. 6 — a. Scaled gene expression of selected Wnt pathway genes in iCMS2_MSS (n = 389), iCMS3_MSS (n = 195) and iCMS3_MSI (n = 116), from TCGA and SG-Bulk datasets. b. Beta-catenin protein levels, by RPPA, in iCMS2_MSS (n = 216), iCMS3_MSS (n = 117) and iCMS3_MSI (n = 67) from TCGA data. P-values for pairwise comparisons are by two-sided Wilcoxon rank-sum test with no correction; overall p-value is by Kruskal-Wallis test. c. Cumulative frequencies of truncating (nonsense and frameshift) APC mutations by position from TCGA and SG-Bulk patients with APC mutations (n = 342), in iCMS2 and iCMS3 (left), iCMS2-MSS vs iCMS3-MSS vs iCMS3-MSI (middle), as well as IMF 5 groups (right). P-value is by two-sided Kolmogorov–Smirnov test. d. Proportion of APC mutation types (left) and regions (right) in samples with APC mutations from TCGA and SG-Bulk data (n = 574). Comparisons are between iCMS2/iCMS3 (top), and iCMS2_MSS/iCMS3_MSS/iCMS3_MSI (bottom). e. APC variant allele frequency (VAF) in iCMS2_MSS (n = 343), iCMS3_MSS (n = 172) and iCMS3_MSI (n = 46) from TCGA data. P-values are by two-sided Wilcoxon rank-sum test with no correction f. Mutational landscape of selected Wnt pathway genes in iCMS2 (left, n = 344) and iCMS3 (right, n = 281) samples in TCGA and SG-Bulk datasets. g. Proportion of samples in TCGA and SG-Bulk datasets (n = 626) with wild type (wt) or mutations (mut) in RNF43 (top) and ZNRF32 (bottom); number of samples in each group is labelled.