Extended Data Fig. 9: Expression analysis.
From: Intra-tumour diversification in colorectal cancer at the single-cell level
a, PCA based on expression pattern of normal organoids from each individual, displaying the first two principal components (n = 13). A subclone and its ancestral clone are circled. b–d, Left, PCA of tumour clones from each individual. Clones derived from different segments are shown in different colours as in Figs. 2–4. A subclone derived from a tumour clone from P2 and its ancestor clone are circled. Right, phylogenetic trees based on expression data (as in Fig. 4b) with the main branches used for our expression analysis indicated. b, P1, n = 20 biologically independent samples. c, P2, n = 22 biologically independent samples. d, P3, n = 17 biologically independent samples. e–g, Global analysis of expression changes attributed to the trunk of the tree, the main branches or subclonal variation. h, Venn diagram displaying the differentially expressed genes that were attributed to the trunk of each tumour. Differentially expressed genes determined by a likelihood ratio test using a negative binomial generalized linear model fit (FDR < 0.05). i–k, Comparison of differentially expressed genes identified in the organoid clones of each patient versus the original tissue sections. Only genes that were significantly altered in all clones or all biopsies from each individual are considered.
