Fig. 7: Association of iCMS markers with polyp subtypes and normal tissues. | Nature Genetics

Fig. 7: Association of iCMS markers with polyp subtypes and normal tissues.

From: Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

Fig. 7

a,b, Heatmaps of tubular adenoma (AD) (a) and SSL (b) marker genes obtained from Chen et al. 44, colored by the average of scaled (z-transformed) expression values of epithelial single cells from five-cohort scRNA-seq data (patients = 61). c, Barplots quantify enrichment of tissue-specific genes in each of the four DEG sets, calculated using the TissueEnrich package (iCMS2 Up: 308; iCMS2 Down: 279; iCMS3 Up: 74; iCMS3 down: 54; total: 715). Red line, P = 0.1. The heatmaps show expression levels of the seven iCMS3-Up DEGs defined as stomach-specific in the TissueEnrich database. Left, scaled expression in diverse tissues. Right, scaled epithelial pseudo-bulk expression in 61 patients. d, Heatmap of gastric metaplasia signature genes, similar to a and b. e, Heatmap of GSEA leading edge genes within crypt top and crypt bottom gene sets, showing scaled epithelial pseudo-bulk expression levels across 61 patients from five scRNA-seq cohorts.

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