Extended Data Fig. 3: Association between tumor antigen expression and Cmai BCR binding scores.
(a) The average BCR binding scores are higher for extracellular tumor antigens that are more highly expressed than for extracellular tumor antigens that are lowly expressed, in each TCGA cohort. N = 822 unique antigens. Sample size (number of patients) in each cohort is: ALL = 64, STES = 30, STAD = 25, BRCA = 26, LUSC = 31, SKCM = 25, LUAD = 24, OV = 21, HNSC = 36, ESCA = 34, KIRC = 19, THCA = 20, TGCT = 22, BLCA = 25, CESC = 29, COAD = 24, PAAD = 38, SARC = 19, KIRP = 19, DLBC = 19, MESO = 21, THYM = 24, PRAD = 21, UVM = 16, CHOL = 31, UCS = 16, LAML = 20, PCPG = 21, KICH = 18, LGG = 19, ACC = 24, GBM = 22. For the boxplot, box boundaries represent interquartile ranges, whiskers extend to the most extreme data point, which is no more than 1.5 times the interquartile range, and the line in the middle of the box represents the median. (b) The correlation between BCR binding scores and tumor antigen expression is higher for extracellular antigens than for intracellular antigens. The “all” group in (a) refers to all 32 TCGA cohorts. Numbers of putative extracellular antigens (N) are: STES = 30, STAD = 25, BRCA = 26, LUSC = 31, SKCM = 25, LUAD = 24, OV = 21, HNSC = 36, ESCA = 34, KIRC = 19, THCA = 20, TGCT = 22, BLCA = 25, CESC = 29, COAD = 24, PAAD = 38, SARC = 19, KIRP = 19, DLBC = 19, MESO = 21, THYM = 24, PRAD = 21, UVM = 16, CHOL = 31, UCS = 16, LAML = 20, PCPG = 21, KICH = 18, LGG = 19, ACC = 24, and GBM = 22. Numbers of putative intracellular antigens (N) are: STES = 30, STAD = 29, BRCA = 22, LUSC = 37, SKCM = 40, LUAD = 24, OV = 22, HNSC = 42, ESCA = 36, KIRC = 19, THCA = 19, TGCT = 64, BLCA = 31, CESC = 33, COAD = 23, PAAD = 25, SARC = 20, KIRP = 20, DLBC = 19, MESO = 19, THYM = 25, PRAD = 21, UVM = 25, CHOL = 25, UCS = 39, LAML = 34, PCPG = 43, KICH = 20, LGG = 32, ACC = 26, and GBM = 33. For (a) and (b), the individual cancer types are ranked as in Fig. 4c.
