{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,7]],"date-time":"2026-06-07T06:49:37Z","timestamp":1780814977462,"version":"3.54.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2019,11,14]],"date-time":"2019-11-14T00:00:00Z","timestamp":1573689600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["LM012487"],"award-info":[{"award-number":["LM012487"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54CA217376"],"award-info":[{"award-number":["U54CA217376"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001109","name":"Flinn Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001109","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Mayo Clinic and Arizona State University Alliance for Health Care Seed Grant"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Functions of cancer driver genes vary substantially across tissues and organs. Distinguishing passenger genes, oncogenes (OGs) and tumor-suppressor genes (TSGs) for each cancer type is critical for understanding tumor biology and identifying clinically actionable targets. Although many computational tools are available to predict putative cancer driver genes, resources for context-aware classifications of OGs and TSGs are limited.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We show that the direction and magnitude of somatic selection of protein-coding mutations are significantly different for passenger genes, OGs and TSGs. Based on these patterns, we develop a new method (genes under selection in tumors) to discover OGs and TSGs in a cancer-type specific manner. Genes under selection in tumors shows a high accuracy (92%) when evaluated via strict cross-validations. Its application to 10\u00a0172 tumor exomes found known and novel cancer drivers with high tissue-specificities. In 11 out of 13 OGs shared among multiple cancer types, we found functional domains selectively engaged in different cancers, suggesting differences in disease mechanisms.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>An R implementation of the GUST algorithm is available at https:\/\/github.com\/liliulab\/gust. A database with pre-computed results is available at https:\/\/liliulab.shinyapps.io\/gust.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz851","type":"journal-article","created":{"date-parts":[[2019,11,12]],"date-time":"2019-11-12T15:10:37Z","timestamp":1573571437000},"page":"1712-1717","source":"Crossref","is-referenced-by-count":46,"title":["Somatic selection distinguishes oncogenes and tumor suppressor genes"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0175-0423","authenticated-orcid":false,"given":"Pramod","family":"Chandrashekar","sequence":"first","affiliation":[{"name":"College of Health Solutions, Arizona State University , Phoenix, AZ, 85004, USA"},{"name":"Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, AZ, 85281, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Navid","family":"Ahmadinejad","sequence":"additional","affiliation":[{"name":"College of Health Solutions, Arizona State University , Phoenix, AZ, 85004, USA"},{"name":"Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, AZ, 85281, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junwen","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Health Solutions, Arizona State University , Phoenix, AZ, 85004, USA"},{"name":"Department of Health Sciences Research & Center for Individualized Medicine , Mayo Clinic Arizona, Scottsdale, AZ, 85259, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksandar","family":"Sekulic","sequence":"additional","affiliation":[{"name":"Department of Health Sciences Research & Center for Individualized Medicine , Mayo Clinic Arizona, Scottsdale, AZ, 85259, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan B","family":"Egan","sequence":"additional","affiliation":[{"name":"Department of Health Sciences Research & Center for Individualized Medicine , Mayo Clinic Arizona, Scottsdale, AZ, 85259, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan W","family":"Asmann","sequence":"additional","affiliation":[{"name":"Department of Health Sciences Research, Mayo Clinic Florida , Jacksonville, AZ, 32224, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sudhir","family":"Kumar","sequence":"additional","affiliation":[{"name":"Institute for Genomics and Evolutionary Medicine, Temple University , Philadelphia, PA, 19122, USA"},{"name":"Department of Biology, Temple University , Philadelphia, PA, 19122, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlo","family":"Maley","sequence":"additional","affiliation":[{"name":"Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, AZ, 85281, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4002-7497","authenticated-orcid":false,"given":"Li","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Health Solutions, Arizona State University , Phoenix, AZ, 85004, USA"},{"name":"Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, AZ, 85281, USA"},{"name":"Department of Health Sciences Research & Center for Individualized Medicine , Mayo Clinic Arizona, Scottsdale, AZ, 85259, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,11,14]]},"reference":[{"key":"2023060912024461900_btz851-B1","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/j.cell.2018.02.060","article-title":"Comprehensive characterization of cancer driver genes and mutations","volume":"173","author":"Bailey","year":"2018","journal-title":"Cell"},{"key":"2023060912024461900_btz851-B2","first-page":"48","article-title":"Epidermal growth factor receptor (EGFR) in lung cancer: an overview and update","volume":"2","author":"Bethune","year":"2010","journal-title":"J. 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