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. 2022 Nov 8;11:e81114. doi: 10.7554/eLife.81114

Figure 9. Multi-omics alteration characteristics of six subtypes.

(A) Genomic alteration landscape according to GINS taxonomy. The mutational genes were selected based on mutation frequency >10% and MutSigCV q-value <0.05. The focal gain and loss regions were selected based on CNV frequency >40% and GISTIC q-value <0.05. The methylation silencing (Methsil) genes were identified based on our pipeline. (B–D) The distribution of fraction of genome alteration (FGA), fraction of genome gained (FGG), and fraction of genome lost (FGL) among six subtypes. Kruskal-Wallis test. (E) Heatmap showed the distribution of broad copy number changes across six subtypes in the TCGA-CRC dataset. (F) The distribution of Ch20 alterations in six subtypes. Kruskal-Wallis test. (G) Sankey plot showed connections among GINS subtypes, CIMP phenotypes, and MSI phenotypes. (H–I) The expression levels of SMOC1 and TMEM106A were significantly inversely correlated with their methylation levels. ***p<0.001, ****p<0.0001.

Figure 9.

Figure 9—figure supplement 1. Genomic alterations of six subtypes.

Figure 9—figure supplement 1.

(A-B) Barplots showed the distribution of KRAS (A) and BRAF (B) mutations to six subtypes in the discovery cohort. (C) Four CpG island methylator phenotype (CIMP) were identified from the TCGA-CRC cohort using the beta value of 5000 CpG island promoters with the most variation.