Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. Ca-a Cancer J Clinicians. 2018;68:394–424.
Zhang PH, Zheng ZG, Ling L, Yang XH, Zhang N, Wang X, et al. w09, a novel autophagy enhancer, induces autophagy-dependent cell apoptosis via activation of the EGFR-mediated RAS-RAF1-MAP2K-MAPK1/3 pathway. Autophagy. 2017;13:1093–112.
Article CAS PubMed PubMed Central Google Scholar
Chung HC, Bang YJ, Fuchs CS, Qin SK, Satoh T, Shitara K, et al. First-line pembrolizumab/placebo plus trastuzumab and chemotherapy in HER2-positive advanced gastric cancer: KEYNOTE-811. Future Oncol. 2021;17:491–501.
Article CAS PubMed Google Scholar
Wang DS, Liu ZX, Lu YX, Bao H, Wu X, Zeng ZL, et al. Liquid biopsies to track trastuzumab resistance in metastatic HER2-positive gastric cancer. Gut. 2019;68:1152–61.
Article CAS PubMed Google Scholar
Lord CJ, Ashworth A. PARP inhibitors: Synthetic lethality in the clinic. Science. 2017;355:1152–8.
Article CAS PubMed PubMed Central Google Scholar
Fong PC, Boss DS, Yap TA, Tutt A, Wu PJ, Mergui-Roelvink M, et al. Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N Engl J Med. 2009;361:123–34.
Article CAS PubMed Google Scholar
Yeoh KG, Tan PT. Mapping the genomic diaspora of gastric cancer. Nat Rev Cancer. 2022;22:71–84.
Article CAS PubMed Google Scholar
Kroll ES, Hyland KM, Hieter P, Li JJ. Establishing genetic interactions by a synthetic dosage lethality phenotype. Genetics. 1996;143:95–102.
Article CAS PubMed PubMed Central Google Scholar
Zecchini V, Frezza C. Metabolic synthetic lethality in cancer therapy. Biochimica Et Biophysica Acta-Bioenerg. 2017;1858:723–31.
Muller FL, Aquilanti EA, DePinho RA. Collateral lethality: a new therapeutic strategy in oncology. Trends Cancer. 2015;1:161–73.
Article PubMed PubMed Central Google Scholar
Jerby-Arnon L, Pfetzer N, Waldman YY, McGarry L, James D, Shanks E, et al. Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality. Cell. 2014;158:1199–209.
Article CAS PubMed Google Scholar
Wang J, Zhang Q, Han J, Zhao Y, Zhao C, Yan B, et al. Computational methods, databases and tools for synthetic lethality prediction. Brief Bioinform. 2022;23:bbac106.
Article PubMed PubMed Central Google Scholar
Sinha S, Thomas D, Chan S, Gao Y, Brunen D, Torabi D, et al. Systematic discovery of mutation-specific synthetic lethals by mining pan-cancer human primary tumor data. Nat Commun. 2017;8:13.
Lee JS, Das A, Jerby-Arnon L, Arafeh R, Auslander N, Davidson M, et al. Harnessing synthetic lethality to predict the response to cancer treatment. Nat Commun. 2018;9:12.
Das S, Deng X, Camphausen K, Shankavaram U. DiscoverSL: an R package for multi-omic data driven prediction of synthetic lethality in cancers. Bioinformatics. 2019;35:701–2.
Article CAS PubMed Google Scholar
Bass AJ, Thorsson V, Shmulevich I, Reynolds SM, Miller M, Bernard B, et al. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014;513:202–9.
Cristescu R, Lee J, Nebozhyn M, Kim KM, Ting JC, Wong SS, et al. Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes. Nat Med. 2015;21:449–U217.
Article CAS PubMed Google Scholar
Lei ZD, Tan IB, Das K, Deng NT, Zouridis H, Pattison S, et al. Identification of molecular subtypes of gastric cancer with different responses to PI3-kinase inhibitors and 5-fluorouracil. Gastroenterology. 2013;145:554–65.
Article CAS PubMed Google Scholar
Yoon SJ, Park J, Shin Y, Choi Y, Park SW, Kang SG, et al. Deconvolution of diffuse gastric cancer and the suppression of CD34 on the BALB/c nude mice model. Bmc Cancer. 2020;20:10.
Ghandi M, Huang FW, Jane-Valbuena J, Kryukov GV, Lo CC, McDonald ER, et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature. 2019;569:503–8.
Article CAS PubMed PubMed Central Google Scholar
Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, et al. Missing value estimation methods for DNA microarrays. Bioinformatics. 2001;17:520–5.
Article CAS PubMed Google Scholar
Meyers RM, Bryan JG, McFarland JM, Weir BA, Sizemore AE, Xu H, et al. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat Genet. 2017;49:1779–84.
Article CAS PubMed PubMed Central Google Scholar
Tsherniak A, Vazquez F, Montgomery PG, Weir BA, Kryukov G, Cowley GS, et al. Defining a Cancer Dependency Map. Cell. 2017;170:564–76.e16.
Article CAS PubMed PubMed Central Google Scholar
Bashashati A, Haffari G, Ding JR, Ha G, Lui K, Rosner J, et al. DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biol. 2012;13:14.
Wu GM, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 2010;11:23.
He CY, Qiu MZ, Yang XH, Zhou DL, Ma JJ, Long YK, et al. Classification of gastric cancer by EBV status combined with molecular profiling predicts patient prognosis. Clin Transl Med. 2020;10:353–62.
Article PubMed PubMed Central Google Scholar
Ge S, Xia X, Ding C, Zhen B, Zhou Q, Feng J, et al. A proteomic landscape of diffuse-type gastric cancer. Nat Commun. 2018;9:1012.
Article PubMed PubMed Central Google Scholar
Wang K, Yuen ST, Xu J, Lee SP, Yan HH, Shi ST, et al. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer. Nat Genet. 2014;46:573–82.
Article CAS PubMed Google Scholar
Lee YS, Cho YS, Lee GK, Lee S, Kim YW, Jho S, et al. Genomic profile analysis of diffuse-type gastric cancers. Genome Biol. 2014;15:R55.
Article PubMed PubMed Central Google Scholar
Cancer Genome Atlas Research, N. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014;513:202–9.
Jeong SH, Park M, Park SY, Park J, Kim TH, Lee YJ, et al. Transcriptome analysis and the prognostic role of NUDC in diffuse and intestinal gastric cancer. Technol Cancer Res Treat. 2021;20:15330338211019501.
Article CAS PubMed PubMed Central Google Scholar
Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, et al. A census of human cancer genes. Nat Rev Cancer. 2004;4:177–83.
Article CAS PubMed PubMed Central Google Scholar
Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene-Sanz A, et al. IntOGen-mutations identifies cancer drivers across tumor types. Nat Methods. 2013;10:1081–2.
Article CAS PubMed PubMed Central Google Scholar
Vogelstein B, Papadopoulos N, Velculescu VE, Zhou SB, Diaz LA, Kinzler KW. Cancer Genome Landscapes. Science. 2013;339:1546–58.
Article CAS PubMed PubMed Central Google Scholar
Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nat Methods. 2013;10:1108–15.
Article CAS PubMed PubMed Central Google Scholar
Huang JK, Jia TQ, Carlin DE, Ideker T. pyNBS: a Python implementation for network-based stratification of tumor mutations. Bioinformatics. 2018;34:2859–61.
Article CAS PubMed PubMed Central Google Scholar
Tan IB, Ivanova T, Lim KH, Ong CW, Deng NT, Lee J, et al. Intrinsic subtypes of gastric cancer, based on gene expression pattern, predict survival and respond differently to chemotherapy. Gastroenterology. 2011;141:476–U551.
Cao J, Gong J, Li XH, Hu ZX, Xu YJ, Shi H, et al. Unsupervised hierarchical clustering identifies immune gene subtypes in gastric cancer. Front Pharmacol. 2021;12:12.
Hanzelmann S, C
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