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. Author manuscript; available in PMC: 2021 Mar 29.
Published in final edited form as: Nat Genet. 2020 Sep 14;52(10):1057–1066. doi: 10.1038/s41588-020-0687-1

Extended Data Fig. 3. Immune escape and antigenicity in TCGA CRC, STAD and UCEC samples.

Extended Data Fig. 3

(a) Prevalence of the individual immune escape mechanisms considered in the combined cohort of CRC, STAD and UCEC samples. P-values shown on top of each bar indicate the result of chi-squared test for that mechanism, corrected for multiple comparisons using the Holm-Bonferroni method. An additional test comparing the presence/absence of any immune checkpoint escape is also indicated above the checkpoint columns. (b-e) Antigen landscape and immune escape characteristics of a combined cohort from TCGA. Figures correspond to Figures 2d–g. Two-sided chi-squared test is indicated on top of (b) and (d). Mann-Whitney tests (c: two-sided, e: one-sided) are reported above (c) and (e). No adjustment for multiple comparisons was made. Violin widths in (c) & (e) represent raw data density with binned individual data-points overlaid on top.