Extended Data Fig. 2: Differences of the cellular composition, distribution and transcriptional states across different tissues.

a, The same UMAP as in Extended Data Fig. 1a, but with cells colored by TGFB1 expression. b–d, Bar graph displaying the composition of B cell subtypes (b) and antibody isotypes (c) across different tissues, and the landscape of antibody isotypes compositions across B cell subtypes (d) in CRC patients and healthy donors. e, Box plots showing the paired comparisons of cell proportions of monocyte and mast cells among matched tissues from the same CRC patients (n = 10). P values are determined by paired two-sided Mann-Whitney test. f, Patients from the TCGA CRC cohort that are ranked by signature score constructed using specific marker genes of mast cells and monocytes. Signature score is defined as the T-test score comparing normalized expression of mast cell markers versus monocyte markers. Samples are divided into 3 approximately equal groups according to the score (upper). The heatmap illustrating the expression of marker genes across tumor samples (middle). Estimates are made for the dependence of all-time risk of death on the signature score (bottom). P value is determined by the cox proportional hazards (CoxPH) model, and the dotted curves represent the 95% confidence interval (CI) of the log hazard ratio. Hi, high; lo, low. g, Unsupervised hierarchical clustering dendrogram of myeloid cells, NK cells and B cells derived from the average transcriptome profiles across tissues in CRC patients and healthy donors. h, Volcano plots illustrating the differentially expressed genes in IELs between colon and ileum of CRC patients (left) and healthy donors (right). Genes with significant differential expression and consistent tendency in CRC patients and healthy donors are indicated in green or purple dots and bold labels. i, Heatmap displaying expression of top DEGs of ileum vs. colon across ileum, colon and tumor in CRC patients and healthy donors. Box plots: center line, median; box limits, first and third quartile; whiskers, 1.5× interquartile range.