Supplemental Figure 5 from TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal

Supplemental Figure 5: (A) Overview of the method to compute differential expression for samples in the integrated pan-cancer group vs. other samples in the TCGA cohort. Tissue composition imbalance was corrected for by performing t-tests within each tissue. For each gene, t-statistics were computed within each tumor type separately and then summarized per-gene t-statistics were calculated as an arithmetic mean, weighted by the inverse variance of the all the tissue-specific t-statistics values. (B) The distribution of log-transformed TPM values estimated from the mRNA-Seq data showing a normal-like distribution. (C) Comparing the log-transformed TPM values of the mRNA-Seq data to a normal distribution shows a reasonable agreement with the tumor data having slightly heavier tails. (D) Venn diagram representing the innate and adaptive immune systems and different levels of evidence supporting higher activity of each of the components of those systems in the pan-cancer cluster when compared to the rest of the TCGA cohort. We found evidence of both innate and adaptive immune system signaling with a number of different analyses. (E) Detailed version of the immune-related pathway characterizing the integrated pan-cancer cluster. This version of the pathway shows additional genes and their connections that are not shown in the summarized version of the immune signaling pathway of Figure 1D of the main text.