Extended Data Fig. 5: Summary of functional properties of various T cell clusters.
From: Lineage tracking reveals dynamic relationships of T cells in colorectal cancer
a, Functional subsets of CD4+ T cell (n = 4,902) clusters defined by a set of known marker genes. Number of cells contained in each CD4+ cluster: TN, n = 462; P.TCM, n = 472; TEMRA, n = 190; N.TCM, n = 388; TRM, n = 568; follicular T helper (TFH), n = 262; TEM, n = 185; TH17, n = 244; TH1-like cells, n = 319; P.Treg, n = 389; N.Treg, n = 103; T.Treg, n = 1,320. N, normal tissue; P, peripheral blood; T, tumour. b, Characteristics of the CD8+ IEL T cells as defined by the expression properties of a panel of functionally relevant genes in CD8+ T cells (n = 3,628). Number of cells contained in each CD8+ cluster: TN, n = 174; TCM, n = 169; TEMRA, n = 743; TEM, n = 773; TRM, n = 487; IEL, n = 351; TEX, n = 860; MAIT, n = 71. For violin plots in a and b, colours denote average expression levels; widths denote cell densities. c, t-SNE plot showing the presence of different T cell clusters in peripheral blood (n = 2,449; CD8+ T cells, n = 1,021; CD4+ T cells, n = 1,428), adjacent normal tissues (n = 1,962; CD8+ T cells, n = 961; CD4+ T cells, n = 1,001) and tumours (n = 4,119; CD8+ T cells, n = 1,646; CD4+ T cells, n = 2,473). d, Overview of T cell cluster characteristics. STARTRAC-dist: +++ indicates Ro/e > 1; ++, 0.8 < Ro/e ≤ 1; +, 0.2 < Ro/e ≤ 0.8; +/−, 0 < Ro/e ≤ 0.2; −, Ro/e = 0. STARTRAC-expa: +++ indicates \({I}_{{\rm{expa}}}^{{\rm{STARTRAC}}}\) > 0.10; ++, 0.06 < \({I}_{{\rm{expa}}}^{{\rm{STARTRAC}}}\) ≤ 0.10; +, 0.005 < \({I}_{{\rm{expa}}}^{{\rm{STARTRAC}}}\) ≤ 0.05; -, \({I}_{{\rm{expa}}}^{{\rm{STARTRAC}}}\) ≤ 0.005. STARTRAC-migr: +++ indicates \({I}_{{\rm{migr}}}^{{\rm{STARTRAC}}}\) > 0.50; ++, 0.21 < \({I}_{{\rm{migr}}}^{{\rm{STARTRAC}}}\) ≤ 0.50; +, 0.1 < \({I}_{{\rm{migr}}}^{{\rm{STARTRAC}}}\) ≤ 0.20; −, \({I}_{{\rm{migr}}}^{{\rm{STARTRAC}}}\) ≤ 0.1. STARTRAC-tran, +++ indicates \({I}_{{\rm{tran}}}^{{\rm{STARTRAC}}}\) > 0.20; ++, 0.10 < \({I}_{{\rm{tran}}}^{{\rm{STARTRAC}}}\) ≤ 0.20; +, 0.05 < \({I}_{{\rm{tran}}}^{{\rm{STARTRAC}}}\) ≤ 0.10; −, \({I}_{{\rm{tran}}}^{{\rm{STARTRAC}}}\) ≤ 0.05.