Extended Data Fig. 3: Immune escape and antigenicity in TCGA CRC, STAD and UCEC samples.
From: Evolutionary dynamics of neoantigens in growing tumors
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 Fig. 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.
