Fig. 2

Overview of reconstructing cancer patient-specific genome-scale metabolic models (GEMs). a Reconstruction of 1056 patient-specific GEMs for 25 cancer types by using the PCAWG and TCGA RNA-seq data. The number of samples for each cancer type is presented in a parenthesis next to the cancer type abbreviations. The presented cancer types are as follows: Biliary-AdenoCA, biliary adenocarcinoma; Bladder-TCC, bladder transitional cell carcinoma; Breast-AdenoCA, breast adenocarcinoma; Breast-LobularCA, breast lobular carcinoma; Cervix-AdenoCA, cervix adenocarcinoma; Cervix-SCC, cervix squamous cell carcinoma; CNS-GBM/Oligo, central nervous system glioblastoma or oligodenroglioma; ColoRect-AdenoCA, colorectal adenocarcinoma; Eso-AdenoCA, esophagus adenocarcinoma; Head-SCC, head-and-neck squamous cell carcinoma; Kidney-ChRCC, kidney chromophobe renal cell carcinoma; Kidney-RCC, kidney renal cell carcinoma; Liver-HCC, liver hepatocellular carcinoma; Lung-AdenoCA, lung adenocarcinoma; Lung-SCC, lung squamous cell carcinoma; Lymph-BNHL, lymphoid mature B-cell lymphoma; Ovary-AdenoCA, ovary adenocarcinoma; Prost-AdenoCA, prostate adenocarcinoma; Skin-Melanoma, skin melanoma; SoftTissue-Leiomyo, leiomyosarcoma of soft tissue; SoftTissue-Liposarc, liposarcoma of soft tissue; Stomach-AdenoCA, stomach adenocarcinoma; TCGA-LAML, acute myeloid leukemia; Thy-AdenoCA, thyroid low-grade adenocarcinoma; and Uterus-AdenoCA, uterus adenocarcinoma. b Number of reactions (pink) and metabolites (purple) across the 1043 GEMs. The model statistics for 1056 GEMs, including the discarded GEMs not presented herein, are available in Additional file 1: Fig. S1. c t-SNE plot of the reaction contents of the 1043 cancer patient-specific GEMs. Same colors are used as presented in a