1. Defining the eTME genes.
Defining the eTME genes. A, The relative expression level of each gene of each previously published signature (Immunome and the complement signature from Winslow) in the immune/stroma component over tumor component. Dotted lines show 3× and 20× cutoffs. B, Aggregated single-cell gene expression normalized by expression of the same gene in the tumor component. “Non-eTME” genes refer to genes not belonging to the eTME genes (3×); “eTME (3×)” and “eTME (20×)” refer to the eTME genes defined with 3× and 20× fold cutoffs. C, eTME gene signatures assigned cell types to 969 cells according to their single-cell RNA-seq data. D, Validation of refined gene signatures using IHC. RNA-seq data from 7 patients were analyzed to predict the immune-cell infiltration levels using gene signatures refined by the eTME criteria for a series of cell types by ssGSEA. IHC was performed on formalin-fixed, paraffin-embedded samples from the same patients for validation. Spearman correlations between them were shown in histograms.
Tao Wang et al. Cancer Discov 2018;8:
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