{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T15:10:09Z","timestamp":1761491409668,"version":"3.37.3"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2022,5,13]],"date-time":"2022-05-13T00:00:00Z","timestamp":1652400000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Fonds Wetenschappelijk Onderzoek-Vlaanderen (FWO","award":["G046318","G.0371.06","3G045620","HBC.2019.2528"],"award-info":[{"award-number":["G046318","G.0371.06","3G045620","HBC.2019.2528"]}]},{"DOI":"10.13039\/100012331","name":"VLAIO","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100012331","id-type":"DOI","asserted-by":"crossref"}]},{"name":"UGent Bijzonder Onderzoeksfonds"},{"name":"the KU Leuven Bijzonder Onderzoeksfonds and the Flemish Government"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,13]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Network-based driver identification methods that can exploit mutual exclusivity typically fail to detect rare drivers because of their statistical rigor. Propagation-based methods in contrast allow recovering rare driver genes, but the interplay between network topology and high-scoring nodes often results in spurious predictions. The specificity of driver gene detection can be improved by taking into account both gene-specific and gene-set properties. Combining these requires a formalism that can adjust gene-set properties depending on the exact network context within which a gene is analyzed.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We developed OMEN: a logic programming framework based on random walk semantics. OMEN presents a number of novel concepts. In particular, its design is unique in that it presents an effective approach to combine both gene-specific driver properties and gene-set properties, and includes a novel method to avoid restrictive, a priori filtering of genes by exploiting the gene-set property of mutual exclusivity, expressed in terms of the functional impact scores of mutations, rather than in terms of simple binary mutation calls. Applying OMEN to a benchmark dataset derived from TCGA illustrates how OMEN is able to robustly identify driver genes and modules of driver genes as proxies of driver pathways.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The source code is freely available for download at www.github.com\/DriesVanDaele\/OMEN. The dataset is archived at https:\/\/doi.org\/10.5281\/zenodo.6419097 and the code at https:\/\/doi.org\/10.5281\/zenodo.6419764.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac312","type":"journal-article","created":{"date-parts":[[2022,5,9]],"date-time":"2022-05-09T19:11:53Z","timestamp":1652123513000},"page":"3245-3251","source":"Crossref","is-referenced-by-count":6,"title":["OMEN: network-based driver gene identification using mutual exclusivity"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5404-4290","authenticated-orcid":false,"given":"Dries","family":"Van Daele","sequence":"first","affiliation":[{"name":"Department of Computer Science, KU Leuven , Leuven 3001, Belgium"}]},{"given":"Bram","family":"Weytjens","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, IMEC , Gent 9000, Belgium"}]},{"given":"Luc","family":"De Raedt","sequence":"additional","affiliation":[{"name":"Department of Computer Science, KU Leuven , Leuven 3001, Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2169-4588","authenticated-orcid":false,"given":"Kathleen","family":"Marchal","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, IMEC , Gent 9000, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2022,5,13]]},"reference":[{"key":"2023041408193066400_","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1016\/j.cell.2015.10.025","article-title":"The molecular taxonomy of primary prostate cancer","volume":"163","author":"Abeshouse","year":"2015","journal-title":"Cell"},{"key":"2023041408193066400_","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s13059-015-0612-6","article-title":"Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations","volume":"16","author":"Babur","year":"2015","journal-title":"Genome Biol"},{"key":"2023041408193066400_","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":"2023041408193066400_","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/nature11154","article-title":"Sequence analysis of mutations and translocations across breast cancer subtypes","volume":"486","author":"Banerji","year":"2012","journal-title":"Nature"},{"key":"2023041408193066400_","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1101\/gr.125567.111","article-title":"Mutual exclusivity analysis identifies oncogenic network modules","volume":"22","author":"Ciriello","year":"2012","journal-title":"Genome Res"},{"key":"2023041408193066400_","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1038\/ng.2762","article-title":"Emerging landscape of oncogenic signatures across human cancers","volume":"45","author":"Ciriello","year":"2013","journal-title":"Nat. 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