Extended Data Fig. 3: Pan-cancer analysis of CCLE samples.
(a, b) Sample distributions of different cell lineages (a) and cancer types (b) in RPPA-based clusters. (c, d) Box plots of MELANA (c) and SGK1 (d) in skin cancer (N = 49) and other cell lines (N = 829). (e) Box plot of BCL2 expression in luminal (N = 11) and other subtypes (N = 37) of breast cancer. (f) Box plot of expression of the proteins involved in the cell cycle in fibroblasts (N = 17) and other cell lines (N = 861). (c-f) N represents the number of cell line samples. (g) Box plots showing the comparison of mRNA-based |log2(FC)| vs. protein-based |log2(FC)| between lineages for the lineage-specific markers. N = 2,312 represents the number of protein-lineage pairs. (c-g) The p-values are based on the two-sided Wilcoxon test. (h) Box plots showing differential fold changes of TP53 mRNA and protein expression between TP53 mutant and wild-type TCGA tumor samples. The p-value is based on the paired Wilcoxon test. N = 30 represents the number of cancer types. (i) Effect of mutations in different P53 domains on P53 protein expression. The p-values are based on Wilcoxon test. (j) Box plots showing differential TP53 mRNA (left) and P53 protein (right) expression in TP53 wild-type samples (N = 159) and those harboring mutations in P53 DNA binding domain (DBD domain; N = 267). (k) Box plots showing differential RPPA expression of P53 between TP53 nonsense mutant (N = 40) and wild-type samples (N = 159). (l) Box plots showing differential gene dependency of TP53 between TP53 mutant (N = 364) and wild-type samples (N = 159). (i-l) N represents the number of cell line samples in each group. (m) A bar plot showing the correlation of gene dependency with PKAA protein and mRNA expression in different cell line lineages. Significant correlations (FDR < 0.1) are marked by an asterisk. (n) A bar plot summarizing the number of lineages in which each protein marker is significantly associated with their gene dependency but not with mRNA (FDR < 0.1). N represents the number of protein markers (phase I: N = 21; phase II: N = 25). (c-l) The middle line in the box is the median, the bottom and top of the box are the first and third quartiles, and the whiskers extend to the 1.5× interquartile range of the lower and the upper quartiles, respectively.
