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We recently proposed Moonlight as a bioinformatics framework to predict driver genes and analyze them in a system-biology-oriented manner based on -omics integration. Moonlight uses gene expression as a primary data source and combines it with patterns related to cancer hallmarks and regulatory networks to identify oncogenic mediators. Once the oncogenic mediators are identified, it is important to include extra levels of evidence, called mechanistic indicators, to identify driver genes and to link the observed gene expression changes to the underlying alteration that promotes them. Such a mechanistic indicator could be for example a mutation in the regulatory regions for the candidate gene. Here, we developed new functionalities and released Moonlight2 to provide the user with a mutation-based mechanistic indicator as a second layer of evidence. These functionalities analyze mutations in a cancer cohort to classify them into driver and passenger mutations. Those oncogenic mediators with at least one driver mutation are retained as the final set of driver genes. We applied Moonlight2 to the basal-like breast cancer subtype, lung adenocarcinoma and thyroid carcinoma using data from The Cancer Genome Atlas. For example, in basal-like breast cancer, we found four oncogenes (COPZ2, SF3B4, KRTCAP2 and POLR2J) and nine tumor suppressor genes (KIR2DL4, KIF26B, ARL15, ARHGAP25, EMCN, GMFG, TPK1, NR5A2 and TEK) containing a driver mutation in their promoter region, possibly explaining their deregulation. Moonlight2R is available at https:\/\/github.com\/ELELAB\/Moonlight2R.<\/jats:p>","DOI":"10.1093\/bib\/bbad274","type":"journal-article","created":{"date-parts":[[2023,8,8]],"date-time":"2023-08-08T08:49:58Z","timestamp":1691484598000},"source":"Crossref","is-referenced-by-count":10,"title":["A workflow to study mechanistic indicators for driver gene prediction with Moonlight"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2815-0425","authenticated-orcid":false,"given":"Mona","family":"Nourbakhsh","sequence":"first","affiliation":[{"name":"Cancer Systems Biology , Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby , Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5026-9337","authenticated-orcid":false,"given":"Astrid","family":"Saksager","sequence":"additional","affiliation":[{"name":"Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark , Lyngby , Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7440-0515","authenticated-orcid":false,"given":"Nikola","family":"Tom","sequence":"additional","affiliation":[{"name":"Cancer Systems Biology , Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby , Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xi Steven","family":"Chen","sequence":"additional","affiliation":[{"name":"University of Miami Miller School of Medicine Department of Public Health Sciences, , Miami, FL 33136 , USA"},{"name":"University of Miami Miller School of Medicine Sylvester Comprehensive Cancer Center, , Miami, FL 33136 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1044-4361","authenticated-orcid":false,"given":"Antonio","family":"Colaprico","sequence":"additional","affiliation":[{"name":"University of Miami Miller School of Medicine Sylvester Comprehensive Cancer Center, , Miami, FL 33136 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6193-2296","authenticated-orcid":false,"given":"Catharina","family":"Olsen","sequence":"additional","affiliation":[{"name":"Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Reproduction and Genetics"},{"name":"Brussels Interuniversity Genomics High Throughput core (BRIGHTcore), VUB-ULB , Brussels 1090 , Belgium"},{"name":"Interuniversity Institute of Bioinformatics in Brussels (IB)2 , Brussels 1050 , Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2529-3594","authenticated-orcid":false,"given":"Matteo","family":"Tiberti","sequence":"additional","affiliation":[{"name":"Cancer Structural Biology , , Copenhagen , Denmark"},{"name":"Danish Cancer Institute , , Copenhagen , Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7376-5894","authenticated-orcid":false,"given":"Elena","family":"Papaleo","sequence":"additional","affiliation":[{"name":"Cancer Systems Biology , Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby , Denmark"},{"name":"Cancer Structural Biology , , Copenhagen , Denmark"},{"name":"Danish Cancer Institute , , Copenhagen , Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,8,7]]},"reference":[{"key":"2023092216533307100_ref1","doi-asserted-by":"crossref","first-page":"209","DOI":"10.3322\/caac.21660","article-title":"Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries","volume":"71","author":"Sung","year":"2021","journal-title":"CA Cancer J Clin"},{"key":"2023092216533307100_ref2","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/S0092-8674(00)81683-9","article-title":"The hallmarks of cancer","volume":"100","author":"Hanahan","year":"2000","journal-title":"Cell"},{"key":"2023092216533307100_ref3","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of cancer: the next 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