Figure 1.

TumorComparer workflow and available tumor samples and cell lines

(A) Weighted similarity between pairs of cancer material is computed using data type-specific datum matrices and weights for each molecular data point (e.g., a mutation in a specific gene). Weights are either derived from data or provided by the user, reflecting an emphasis on particular genomic alterations. The weighted similarities for each data type are then normalized and combined into a final weighted similarity score. To compare cell lines and tumors, we used mutations, CNAs, and gene expression (mRNA) values, and chose weights for these features based on the recurrence of cancer type-specific (or pan-cancer) events in sets of tumors samples, as a proxy for the likelihood of the feature to be functional (e.g., to be “drivers”); for expression, we chose the log-fold change in expression in relation to pooled normals. Top: mutated, green; wild type, white. Middle: gains, light and dark red; losses, light and dark blue; diploid, white. Bottom: overexpressed, red; underexpressed, blue.

(B) The number of TCGA tumors and CCLP cell lines for each cancer type included in this study. CCLP, Cancer Cell Line Project; BLCA, bladder urothelial carcinoma; BRCA, breast invasive carcinoma; CESC, cervical squamous cell carcinoma and endocervical adenocarcinoma; COAD, colon adenocarcinoma; DLBC, lymphoid neoplasm diffuse large B cell lymphoma; ESCA, esophageal adenocarcinoma; GBM, glioblastoma multiforme; HNSC, head and neck squamous cell carcinoma; KIRC, kidney renal clear cell carcinoma; LAML, acute myeloid leukemia; LGG, brain lower grade glioma; LIHC, liver hepatocellular carcinoma; LUAD, lung adenocarcinoma; LUSC, lung squamous cell carcinoma; OV, ovarian serous cystadenocarcinoma; PAAD, pancreatic adenocarcinoma; PRAD, prostate adenocarcinoma; READ, rectum adenocarcinoma; SKCM, skin cutaneous melanoma; STAD, stomach adenocarcinoma; TCGA, The Cancer Genome Atlas; THCA, thyroid carcinoma; UCEC, uterine corpus endometrial carcinoma.