Construction of TME signatures and functional annotation.

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Construction of TME signatures and functional annotation. Construction of TME signatures and functional annotation. A, Unsupervised analysis and hierarchical clustering of common DEGs based on expression data derived from the ACRG cohort to classify patients into three groups: Gene clusters A–C. Immuno-group (immunophenotype from previous study; ref. 7), survival status, ACRG subtype, MSI status, histologic subtype, and TMEcluster are shown as patient annotations. B, Kaplan–Meier curves for the three groups of patients. Gene cluster A (n = 64), B (n = 158), and C (n = 77). Log-rank test showed an overall P < 0.001. C and D, GO enrichment analysis of the two TME relevant signature genes—TME signature gene (C) A and (D) B. The x axis indicates the number of genes within each GO term. E, The fraction of TME cells in three gene clusters. Within each group, the scattered dots represent TME cell expression values. We also plotted the Immunoscore of three gene clusters. The thick line represents the median value. The bottom and top of the boxes are the 25th and 75th percentiles (interquartile range). The whiskers encompass 1.5 times the interquartile range. The statistical difference of three gene clusters was compared through the Kruskal–Wallis test. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. Dongqiang Zeng et al. Cancer Immunol Res 2019;7:737-750 ©2019 by American Association for Cancer Research