Fig. 1. Mutation and leukocyte fraction correction.

a The schematic workflow of our study. b Diagram of “mutation correction” that accounts for the functional reduction of protein-coding genes caused by non-synonymous mutations. The gene in the example is more active in tumor 2 than in tumor 1, despite being more highly expressed in tumor 1 due to multiple non-synonymous mutations impairing the function of the protein in tumor 1. c Diagram of “leukocyte fraction correction” that removes the confounding effect of immune cell proportions on the measuring activity of immune-related genes with RNA-seq. Although the same number of total transcripts of a gene are detected in the two tumors, the gene is more actively transcribed on average in tumor 2 than in tumor 1 due to a smaller number of tumor-infiltrating immune cells in tumor 2.