Fig. 3: Comparison of transcriptomics between cancer cell lines and TCGA cohorts, HPA tissues, and single-cell types.

a Dot plot showing the significance (estimated by hypergeometric testing) of the overlapping genes between the enriched genes in CLDs (y-axis) and TCGA cohorts, HPA tissues, and single-cell types (x-axis). P-values were adjusted based on the Benjamini-Hochberg procedure. Non-significant overlaps (adj. P-value > 0.05) are not shown in the figure, and CLDs that are not significantly overlapped with any TCGA cohorts, tissues, single-cell types, or the other way around, are removed. b Venn diagram showing the intersected genes between the enriched genes in cell line-based liver cancer and the TCGA liver cancer, HPA-analyzed liver tissue, and hepatocytes in single-cell type analysis. c Correlation between the CLDs and TCGA cohorts calculated based on the average expression per CLD and TCGA cohort. For each CLD, we used one-sided one-sample Wilcoxon signed-rank test to investigate if the correlations to its unmatched TCGA cohorts were significantly lower than the correlation to its matched TCGA cohort. Based on the information in Supplementary Data 4, 26 statistical tests were performed. *P < 0.05. d Correlation between cell lines by different categorizations. Primary: correlations between primary cell lines. Correlations between cell lines were calculated per cancer type and were summarized (n = 7,189 correlations). Metastatic—same disease: correlations between metastatic cell lines. Correlations between cell lines were calculated per cancer type and were summarized (n = 6,864 correlations). Metastatic—same site: correlations between metastatic cell lines. Correlations between cell lines were calculated per sample collection site and were summarized (n = 7,627 correlations). Statistical significance was evaluated by two-sided Wilcoxon rank-sum test. The lower, middle, and upper hinges correspond to the 25th, 50th, and 75th percentiles. The upper whisker extends from the hinge to the largest value no further than 1.5 * IQR from the hinge (where IQR is the inter-quartile range, or distance between the first and third quartiles). The lower whisker extends from the hinge to the smallest value at most 1.5 * IQR of the hinge. Source data are provided as a Source Data file.