{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T17:52:25Z","timestamp":1774893145589,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2019,10,10]],"date-time":"2019-10-10T00:00:00Z","timestamp":1570665600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005010","name":"Italian Association for Cancer Research","doi-asserted-by":"publisher","award":["20322"],"award-info":[{"award-number":["20322"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005010","name":"Italian Association for Cancer Research","doi-asserted-by":"publisher","award":["18137"],"award-info":[{"award-number":["18137"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>CancerGeneNet (https:\/\/signor.uniroma2.it\/CancerGeneNet\/) is a resource that links genes that are frequently mutated in cancers to cancer phenotypes. The resource takes advantage of a curation effort aimed at embedding a large fraction of the gene products that are found altered in cancer cells into a network of causal protein relationships. Graph algorithms, in turn, allow to infer likely paths of causal interactions linking cancer associated genes to cancer phenotypes thus offering a rational framework for the design of strategies to revert disease phenotypes. CancerGeneNet bridges two interaction layers by connecting proteins whose activities are affected by cancer drivers to proteins that impact on the \u2018hallmarks of cancer\u2019. In addition, CancerGeneNet annotates curated pathways that are relevant to rationalize the pathological consequences of cancer driver mutations in selected common cancers and \u2018MiniPathways\u2019 illustrating regulatory circuits that are frequently altered in different cancers.<\/jats:p>","DOI":"10.1093\/nar\/gkz871","type":"journal-article","created":{"date-parts":[[2019,10,1]],"date-time":"2019-10-01T00:10:47Z","timestamp":1569888647000},"page":"D416-D421","source":"Crossref","is-referenced-by-count":42,"title":["CancerGeneNet: linking driver genes to cancer hallmarks"],"prefix":"10.1093","volume":"48","author":[{"given":"Marta","family":"Iannuccelli","sequence":"first","affiliation":[{"name":"Department of Biology, University of Rome, Tor Vergata, 00133 Rome, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1180-0359","authenticated-orcid":false,"given":"Elisa","family":"Micarelli","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Rome, Tor Vergata, 00133 Rome, Italy"}]},{"given":"Prisca Lo","family":"Surdo","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Rome, Tor Vergata, 00133 Rome, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1300-5479","authenticated-orcid":false,"given":"Alessandro","family":"Palma","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Rome, Tor Vergata, 00133 Rome, Italy"}]},{"given":"Livia","family":"Perfetto","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Rome, Tor Vergata, 00133 Rome, Italy"},{"name":"European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK"}]},{"given":"Ilaria","family":"Rozzo","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Rome, Tor Vergata, 00133 Rome, Italy"}]},{"given":"Luisa","family":"Castagnoli","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Rome, Tor Vergata, 00133 Rome, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5084-9000","authenticated-orcid":false,"given":"Luana","family":"Licata","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Rome, Tor Vergata, 00133 Rome, Italy"}]},{"given":"Gianni","family":"Cesareni","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Rome, Tor Vergata, 00133 Rome, Italy"},{"name":"IRCSS Fondazione Santa Lucia, 00142 Rome, Italy"}]}],"member":"286","published-online":{"date-parts":[[2019,10,10]]},"reference":[{"key":"2020010521384696500_B1","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.cell.2018.03.042","article-title":"The cancer genome Atlas: creating lasting value beyond its data","volume":"173","author":"Hutter","year":"2018","journal-title":"Cell"},{"key":"2020010521384696500_B2","doi-asserted-by":"crossref","first-page":"D941","DOI":"10.1093\/nar\/gky1015","article-title":"COSMIC: the catalogue of somatic mutations in cancer","volume":"47","author":"Tate","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020010521384696500_B3","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1038\/s41568-018-0060-1","article-title":"The COSMIC cancer gene Census: describing genetic dysfunction across all human cancers","volume":"18","author":"Sondka","year":"2018","journal-title":"Nat. Rev. Cancer"},{"key":"2020010521384696500_B4","doi-asserted-by":"crossref","first-page":"D948","DOI":"10.1093\/nar\/gky868","article-title":"The comparative toxicogenomics Database: update 2019","volume":"47","author":"Davis","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020010521384696500_B5","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1038\/nmeth.2642","article-title":"IntOGen-mutations identifies cancer drivers across tumor types","volume":"10","author":"Gonzalez-Perez","year":"2013","journal-title":"Nat. Methods"},{"key":"2020010521384696500_B6","doi-asserted-by":"crossref","first-page":"D975","DOI":"10.1093\/nar\/gkv1314","article-title":"DriverDBv2: a database for human cancer driver gene research","volume":"44","author":"Chung","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2020010521384696500_B7","doi-asserted-by":"crossref","first-page":"2699","DOI":"10.1093\/nar\/gky092","article-title":"UniProt: the universal protein knowledgebase","volume":"46","author":"UniProt Consortium, T","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020010521384696500_B8","doi-asserted-by":"crossref","first-page":"D833","DOI":"10.1093\/nar\/gkw943","article-title":"DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants","volume":"45","author":"Pi\u00f1ero","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020010521384696500_B9","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of Cancer: the next generation","volume":"144","author":"Hanahan","year":"2011","journal-title":"Cell"},{"key":"2020010521384696500_B10","doi-asserted-by":"crossref","first-page":"D548","DOI":"10.1093\/nar\/gkv1048","article-title":"SIGNOR: a database of causal relationships between biological entities","volume":"44","author":"Perfetto","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2020010521384696500_B11","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/s12918-017-0464-7","article-title":"A systematic analysis of FDA-approved anticancer drugs","volume":"11","author":"Sun","year":"2017","journal-title":"BMC Syst. Biol."},{"key":"2020010521384696500_B12","doi-asserted-by":"crossref","first-page":"2684","DOI":"10.1093\/bioinformatics\/bty188","article-title":"SPV: a JavaScript Signaling Pathway Visualizer","volume":"34","author":"Calderone","year":"2018","journal-title":"Bioinformatics"},{"key":"2020010521384696500_B13","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Cs\u00e1rdi","year":"2006","journal-title":"Inter. J. Comp. Syst."},{"key":"2020010521384696500_B14","first-page":"11","article-title":"Exploring network structure, dynamics, and function using NetworkX","volume-title":"Proceedings of the 7th Python in Science Conference","author":"Hagberg","year":"2008"},{"key":"2020010521384696500_B15","doi-asserted-by":"crossref","first-page":"D649","DOI":"10.1093\/nar\/gkx1132","article-title":"The reactome pathway knowledgebase","volume":"46","author":"Fabregat","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020010521384696500_B16","doi-asserted-by":"crossref","first-page":"btv557","DOI":"10.1093\/bioinformatics\/btv557","article-title":"Cytoscape.js: a graph theory library for visualisation and analysis","volume":"32","author":"Franz","year":"2015","journal-title":"Bioinformatics"},{"key":"2020010521384696500_B17","doi-asserted-by":"crossref","first-page":"3779","DOI":"10.1093\/bioinformatics\/btz132","article-title":"CausalTAB:the PSI-MITAB2.8updated format for signalling data representation and dissemination","volume":"35","author":"Perfetto","year":"2019","journal-title":"Bioinformatics"},{"key":"2020010521384696500_B18","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1038\/nmeth.2561","article-title":"mentha: a resource for browsing integrated protein-interaction networks","volume":"10","author":"Calderone","year":"2013","journal-title":"Nat. Methods"},{"key":"2020010521384696500_B19","doi-asserted-by":"crossref","first-page":"D527","DOI":"10.1093\/nar\/gkx876","article-title":"DISNOR: a disease network open resource","volume":"46","author":"Lo\u00a0Surdo","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020010521384696500_B20","doi-asserted-by":"crossref","first-page":"C494","DOI":"10.1152\/ajpcell.00458.2004","article-title":"Caveolin-1 in oncogenic transformation, cancer, and metastasis","volume":"288","author":"Williams","year":"2005","journal-title":"Am. J. Physiol. Physiol."},{"key":"2020010521384696500_B21","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1016\/j.coph.2011.03.009","article-title":"The dual role of autophagy in cancer","volume":"11","author":"Eskelinen","year":"2011","journal-title":"Curr. Opin. Pharmacol."},{"key":"2020010521384696500_B22","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/j.ccr.2011.03.023","article-title":"Ptpn11\/Shp2 acts as a tumor suppressor in hepatocellular carcinogenesis","volume":"19","author":"Bard-Chapeau","year":"2011","journal-title":"Cancer Cell"},{"key":"2020010521384696500_B23","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1016\/j.canlet.2015.01.020","article-title":"PTP1B promotes cell proliferation and metastasis through activating src and ERK1\/2 in non-small cell lung cancer","volume":"359","author":"Liu","year":"2015","journal-title":"Cancer Lett."},{"key":"2020010521384696500_B24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.5402\/2012\/381428","article-title":"The dual role of TGF\u03b2 in human Cancer: From tumor suppression to cancer metastasis","volume":"2012","author":"Neel","year":"2012","journal-title":"ISRN Mol. Biol."},{"key":"2020010521384696500_B25","doi-asserted-by":"crossref","first-page":"eaan2507","DOI":"10.1126\/science.aan2507","article-title":"A pathology atlas of the human cancer transcriptome","volume":"357","author":"Uhlen","year":"2017","journal-title":"Science"},{"key":"2020010521384696500_B26","doi-asserted-by":"crossref","first-page":"e160","DOI":"10.1038\/oncsis.2015.19","article-title":"Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps","volume":"4","author":"Kuperstein","year":"2015","journal-title":"Oncogenesis"},{"key":"2020010521384696500_B27","doi-asserted-by":"crossref","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","article-title":"KEGG: new perspectives on genomes, pathways, diseases and drugs","volume":"45","author":"Kanehisa","year":"2017","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D416\/31697843\/gkz871.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D416\/31697843\/gkz871.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,1,5]],"date-time":"2020-01-05T21:40:29Z","timestamp":1578260429000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/D1\/D416\/5584570"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,10,10]]},"references-count":27,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2019,10,10]]},"published-print":{"date-parts":[[2020,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz871","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,1,8]]},"published":{"date-parts":[[2019,10,10]]}}}