{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T07:14:36Z","timestamp":1784013276739,"version":"3.55.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2022,4,18]],"date-time":"2022-04-18T00:00:00Z","timestamp":1650240000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62002234"],"award-info":[{"award-number":["62002234"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61902380"],"award-info":[{"award-number":["61902380"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021171","name":"Guangdong Basic and Applied Basic Research Foundation","doi-asserted-by":"publisher","award":["2019A1515111180"],"award-info":[{"award-number":["2019A1515111180"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Foundation of SZU","award":["827-000393"],"award-info":[{"award-number":["827-000393"]}]},{"DOI":"10.13039\/501100005090","name":"Beijing Nova Program","doi-asserted-by":"publisher","award":["Z201100006820061"],"award-info":[{"award-number":["Z201100006820061"]}],"id":[{"id":"10.13039\/501100005090","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Each type of cancer usually has several subtypes with distinct clinical implications, and therefore the discovery of cancer subtypes is an important and urgent task in disease diagnosis and therapy. Using single-omics data to predict cancer subtypes is difficult because genomes are dysregulated and complicated by multiple molecular mechanisms, and therefore linking cancer genomes to cancer phenotypes is not an easy task. Using multi-omics data to effectively predict cancer subtypes is an area of much interest; however, integrating multi-omics data is challenging. Here, we propose a novel method of multi-omics data integration for clustering to identify cancer subtypes (MDICC) that integrates new affinity matrix and network fusion methods. Our experimental results show the effectiveness and generalization of the proposed MDICC model in identifying cancer subtypes, and its performance was better than those of currently available state-of-the-art clustering methods. Furthermore, the survival analysis demonstrates that MDICC delivered comparable or even better results than many typical integrative methods.<\/jats:p>","DOI":"10.1093\/bib\/bbac132","type":"journal-article","created":{"date-parts":[[2022,3,21]],"date-time":"2022-03-21T12:08:20Z","timestamp":1647864500000},"source":"Crossref","is-referenced-by-count":55,"title":["MDICC: novel method for multi-omics data integration and cancer subtype identification"],"prefix":"10.1093","volume":"23","author":[{"given":"Ying","family":"Yang","sequence":"first","affiliation":[{"name":"College of Mathematics and Statistics, Shenzhen University, 518000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sha","family":"Tian","sequence":"additional","affiliation":[{"name":"College of Mathematics and Statistics, Shenzhen University, 518000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yushan","family":"Qiu","sequence":"additional","affiliation":[{"name":"College of Mathematics and Statistics, Shenzhen University, 518000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pu","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Life and Health Sciences, Northeastern University, Shenyang, 110169, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quan","family":"Zou","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610056, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,4,18]]},"reference":[{"issue":"8","key":"2022051813451286900_ref1","doi-asserted-by":"crossref","first-page":"2724","DOI":"10.1073\/pnas.1018854108","article-title":"Subtype and pathway specific responses to anticancer compounds in breast cancer","volume":"109","author":"Heiser","year":"2012","journal-title":"Proc Natl Acad Sci"},{"issue":"5","key":"2022051813451286900_ref2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/bcr2635","article-title":"Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer","volume":"12","author":"Prat","year":"2010","journal-title":"Breast Cancer Res"},{"issue":"13","key":"2022051813451286900_ref3","doi-asserted-by":"crossref","first-page":"1858","DOI":"10.1093\/bioinformatics\/btu128","article-title":"A personalized committee classification approach to improving prediction of breast cancer metastasis","volume":"30","author":"Jahid","year":"2014","journal-title":"Bioinformatics"},{"issue":"7592","key":"2022051813451286900_ref4","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/nature16965","article-title":"Genomic analyses identify molecular subtypes of pancreatic cancer","volume":"531","author":"Bailey","year":"2016","journal-title":"Nature"},{"issue":"8","key":"2022051813451286900_ref5","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1038\/nm.3915","article-title":"Toward understanding and exploiting tumor heterogeneity","volume":"21","author":"Alizadeh","year":"2015","journal-title":"Nat Med"},{"issue":"5","key":"2022051813451286900_ref6","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1056\/NEJMra072367","article-title":"Oncogenes and cancer","volume":"358","author":"Carlo M Croce","year":"2008","journal-title":"New England journal of medicine"},{"key":"2022051813451286900_ref7","doi-asserted-by":"crossref","first-page":"84","DOI":"10.3389\/fgene.2017.00084","article-title":"More is better: recent progress in multi-omics data integration methods","volume":"8","author":"Huang","year":"2017","journal-title":"Front Genet"},{"issue":"11","key":"2022051813451286900_ref8","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1177\/1947601910396213","article-title":"Microrna in cancer: the involvement of aberrant microrna biogenesis regulatory pathways","volume":"1","author":"Davis-Dusenbery","year":"2010","journal-title":"Genes Cancer"},{"issue":"5","key":"2022051813451286900_ref9","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1016\/j.ccr.2010.03.017","article-title":"Identification of a cpg island methylator phenotype that defines a distinct subgroup of glioma","volume":"17","author":"Noushmehr","year":"2010","journal-title":"Cancer Cell"},{"issue":"7605","key":"2022051813451286900_ref10","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/nature17676","article-title":"Landscape of somatic mutations in 560 breast cancer whole-genome sequences","volume":"534","author":"Nik-Zainal","year":"2016","journal-title":"Nature"},{"issue":"2","key":"2022051813451286900_ref11","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/j.cell.2013.09.034","article-title":"The somatic genomic landscape of glioblastoma","volume":"155","author":"Brennan","year":"2013","journal-title":"Cell"},{"issue":"7043","key":"2022051813451286900_ref12","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1038\/nature03702","article-title":"Microrna expression profiles classify human cancers","volume":"435","author":"Lu","year":"2005","journal-title":"Nature"},{"issue":"5853","key":"2022051813451286900_ref13","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1126\/science.1145720","article-title":"The genomic landscapes of human breast and colorectal cancers","volume":"318","author":"Wood","year":"2007","journal-title":"Science"},{"issue":"7187","key":"2022051813451286900_ref14","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nature06914","article-title":"Translating insights from the cancer genome into clinical practice","volume":"452","author":"Chin","year":"2008","journal-title":"Nature"},{"issue":"8","key":"2022051813451286900_ref15","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1038\/nrc1414","article-title":"Integrated global profiling of cancer","volume":"4","author":"Hanash","year":"2004","journal-title":"Nat Rev Cancer"},{"issue":"7407","key":"2022051813451286900_ref16","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1038\/nature11252","article-title":"Comprehensive molecular characterization of human colon and rectal cancer","volume":"487","author":"Cancer Genome Atlas Network","year":"2012","journal-title":"Nature"},{"issue":"5","key":"2022051813451286900_ref17","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbaa440","article-title":"Prediction of rna-binding protein and alternative splicing event associations during epithelial\u2013mesenchymal transition based on inductive matrix completion","volume":"22","author":"Qiu","year":"2021","journal-title":"Brief Bioinform"},{"issue":"6","key":"2022051813451286900_ref18","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab332","article-title":"Matrix factorization-based data fusion for the prediction of rna-binding proteins and alternative splicing event associations during epithelial\u2013mesenchymal transition","volume":"22","author":"Qiu","year":"2021","journal-title":"Brief Bioinform"},{"issue":"9","key":"2022051813451286900_ref19","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1261\/rna.074187.119","article-title":"A combinatorially regulated rna splicing signature predicts breast cancer emt states and patient survival","volume":"26","author":"Qiu","year":"2020","journal-title":"RNA"},{"issue":"3","key":"2022051813451286900_ref20","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nmeth.2810","article-title":"Similarity network fusion for aggregating data types on a genomic scale","volume":"11","author":"Wang","year":"2014","journal-title":"Nat Methods"},{"issue":"2","key":"2022051813451286900_ref21","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/nrg3868","article-title":"Methods of integrating data to uncover genotype\u2013phenotype interactions","volume":"16","author":"Ritchie","year":"2015","journal-title":"Nat Rev Genet"},{"issue":"2","key":"2022051813451286900_ref22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1752-0509-8-S2-I1","article-title":"Data integration in the era of omics: current and future challenges","volume":"8","author":"Gomez-Cabrero","year":"2014","journal-title":"BMC Syst Biol"},{"issue":"22","key":"2022051813451286900_ref23","doi-asserted-by":"crossref","first-page":"2906","DOI":"10.1093\/bioinformatics\/btp543","article-title":"Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis","volume":"25","author":"Shen","year":"2009","journal-title":"Bioinformatics"},{"key":"2022051813451286900_ref24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-020-02015-1","article-title":"Mofa+: a statistical framework for comprehensive integration of multi-modal single-cell data","volume":"21","author":"Argelaguet","year":"2020","journal-title":"Genome Biol"},{"issue":"1","key":"2022051813451286900_ref25","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1093\/biostatistics\/kxx017","article-title":"A fully bayesian latent variable model for integrative clustering analysis of multi-type omics data","volume":"19","author":"Mo","year":"2018","journal-title":"Biostatistics"},{"key":"2022051813451286900_ref26","first-page":"252","volume-title":"Proceedings of the 2013 SIAM international conference on data mining","author":"Liu","year":"2013"},{"issue":"16","key":"2022051813451286900_ref27","doi-asserted-by":"crossref","first-page":"2843","DOI":"10.1093\/bioinformatics\/bty1049","article-title":"Pinsplus: a tool for tumor subtype discovery in integrated genomic data","volume":"35","author":"Nguyen","year":"2019","journal-title":"Bioinformatics"},{"issue":"18","key":"2022051813451286900_ref28","doi-asserted-by":"crossref","first-page":"3348","DOI":"10.1093\/bioinformatics\/btz058","article-title":"Nemo: cancer subtyping by integration of partial multi-omic data","volume":"35","author":"Rappoport","year":"2019","journal-title":"Bioinformatics"},{"issue":"1","key":"2022051813451286900_ref29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-018-06921-8","article-title":"Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival","volume":"9","author":"Ramazzotti","year":"2018","journal-title":"Nat Commun"},{"key":"2022051813451286900_ref30","doi-asserted-by":"crossref","first-page":"744","DOI":"10.3389\/fgene.2019.00744","article-title":"Multi-view subspace clustering analysis for aggregating multiple heterogeneous omics data","volume":"10","author":"Shi","year":"2019","journal-title":"Front Genet"},{"key":"2022051813451286900_ref31","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1109\/BIBM.2017.8217682","volume-title":"2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","author":"Ma","year":"2017"},{"issue":"5","key":"2022051813451286900_ref32","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab057","article-title":"Defusion: a denoised network regularization framework for multi-omics integration","volume":"22","author":"Wang","year":"2021","journal-title":"Brief Bioinform"},{"issue":"1","key":"2022051813451286900_ref33","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-021-04195-4","article-title":"Clustering of cancer data based on stiefel manifold for multiple views","volume":"22","author":"Tian","year":"2021","journal-title":"BMC bioinformatics"},{"issue":"8","key":"2022051813451286900_ref34","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1093\/bioinformatics\/btw770","article-title":"Lrssl: predict and interpret drug\u2013disease associations based on data integration using sparse subspace learning","volume":"33","author":"Liang","year":"2017","journal-title":"Bioinformatics"},{"key":"2022051813451286900_ref35","first-page":"1601","volume-title":"Proceedings of the 17th International Conference on Neural Information Processing Systems","author":"Zelnik-Manor","year":"2004"},{"key":"2022051813451286900_ref36","first-page":"3305","article-title":"Unsupervised learning from noisy networks with applications to hi-c data","volume":"29","author":"Wang","year":"2016","journal-title":"Advances in Neural Information Processing Systems"},{"issue":"20","key":"2022051813451286900_ref37","doi-asserted-by":"crossref","first-page":"10546","DOI":"10.1093\/nar\/gky889","article-title":"Multi-omic and multi-view clustering algorithms: review and cancer benchmark","volume":"46","author":"Rappoport","year":"2018","journal-title":"Nucleic Acids Res"},{"issue":"5439","key":"2022051813451286900_ref38","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1126\/science.286.5439.531","article-title":"Molecular classification of cancer: class discovery and class prediction by gene expression monitoring","volume":"286","author":"Golub","year":"1999","journal-title":"Science"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/3\/bbac132\/43745673\/bbac132.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/3\/bbac132\/43745673\/bbac132.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,19]],"date-time":"2023-11-19T02:55:19Z","timestamp":1700362519000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbac132\/6569541"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,4,18]]},"references-count":38,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2022,5,13]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbac132","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,5]]},"published":{"date-parts":[[2022,4,18]]},"article-number":"bbac132"}}