{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T06:53:03Z","timestamp":1790751183680,"version":"4.1.0"},"reference-count":69,"publisher":"SAGE Publications","license":[{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Bioinform Biol Insights"],"published-print":{"date-parts":[[2018,1,1]]},"abstract":"<jats:p>Integrated omics is becoming a new channel for investigating the complex molecular system in modern biological science and sets a foundation for systematic learning for precision medicine. The statistical\/machine learning methods that have emerged in the past decade for integrated omics are not only innovative but also multidisciplinary with integrated knowledge in biology, medicine, statistics, machine learning, and artificial intelligence. Here, we review the nontrivial classes of learning methods from the statistical aspects and streamline these learning methods within the statistical learning framework. The intriguing findings from the review are that the methods used are generalizable to other disciplines with complex systematic structure, and the integrated omics is part of an integrated information science which has collated and integrated different types of information for inferences and decision making. We review the statistical learning methods of exploratory and supervised learning from 42 publications. We also discuss the strengths and limitations of the extended principal component analysis, cluster analysis, network analysis, and regression methods. Statistical techniques such as penalization for sparsity induction when there are fewer observations than the number of features and using Bayesian approach when there are prior knowledge to be integrated are also included in the commentary. For the completeness of the review, a table of currently available software and packages from 23 publications for omics are summarized in the appendix.<\/jats:p>","DOI":"10.1177\/1177932218759292","type":"journal-article","created":{"date-parts":[[2018,2,21]],"date-time":"2018-02-21T01:25:51Z","timestamp":1519176351000},"update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":54,"title":["Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science)"],"prefix":"10.1177","volume":"12","author":[{"given":"Irene Sui Lan","family":"Zeng","sequence":"first","affiliation":[{"name":"Department of Statistics, Faculty of Science, The University of Auckland, Auckland, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Lumley","sequence":"additional","affiliation":[{"name":"Department of Statistics, Faculty of Science, The University of Auckland, Auckland, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2018,2,20]]},"reference":[{"key":"bibr46-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1002\/gepi.21808"},{"key":"bibr47-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1089\/big.2015.0057"},{"key":"bibr48-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-39437-9_4"},{"key":"bibr49-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-6-139"},{"key":"bibr50-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/s13040-015-0052-6"},{"key":"bibr51-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003983"},{"key":"bibr52-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp515"},{"key":"bibr53-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0016345"},{"key":"bibr54-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq071"},{"key":"bibr55-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv770"},{"key":"bibr56-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq583"},{"key":"bibr57-1177932218759292","unstructured":"specmine [computer program]. Version 1.0: R; 2015. https:\/\/github.com\/cran\/specmine"},{"key":"bibr58-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts439"},{"key":"bibr59-1177932218759292","unstructured":"XMRF [computer program]. Version 1.0: R; 2015. https:\/\/cran.r-project.org\/web\/packages\/XMRF"},{"key":"bibr60-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-015-0708-8"},{"key":"bibr61-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-7-74"},{"key":"bibr62-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-7-64"},{"key":"bibr63-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq594"},{"key":"bibr64-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/2041-1480-3-11"},{"key":"bibr65-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq675"},{"key":"bibr66-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr351"},{"key":"bibr67-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1016\/j.biosystems.2011.04.003"},{"key":"bibr68-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-015-0577-1"},{"key":"bibr69-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/1756-0381-6-23"},{"key":"bibr1-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-28062-7_4"},{"key":"bibr2-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1016\/j.chemolab.2012.08.011"},{"key":"bibr3-1177932218759292","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/bioinformatics\/btv544","volume":"32","author":"Yang Z","year":"2015","journal-title":"Bioinformatics"},{"key":"bibr4-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1016\/j.chemolab.2010.08.008"},{"key":"bibr5-1177932218759292","first-page":"391","volume-title":"Multivariate Analysis","volume":"1966","author":"Wold H"},{"key":"bibr6-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1002\/cem.1180040111"},{"key":"bibr7-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1016\/j.chemolab.2010.06.004"},{"key":"bibr8-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-015-0680-3"},{"key":"bibr9-1177932218759292","unstructured":"Su H, Shen Y, Xing F, et al. Robust automatic breast cancer staging using a combination of functional genomics and image-omics. Paper presented at: 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC); August 25-29, 2015; Milan, Italy."},{"key":"bibr10-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-117"},{"key":"bibr11-1177932218759292","doi-asserted-by":"crossref","unstructured":"Aibar S, Abaigar M, Campos-Laborie F, S\u00e1nchez-Santos J, Hernandez-Rivas J, Las Rivas J. Identification of expression patterns in the progression of disease stages by integration of transcriptomic data. Paper presented at: Statistical Methods for Omics Data Integration and Analysis; September 7-11, 2015; Valencia, Spain.","DOI":"10.1186\/s12859-016-1290-4"},{"key":"bibr12-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1214\/12-AOAS578"},{"key":"bibr13-1177932218759292","volume-title":"Statistical Learning Methods for Omics Data Integration in Dimension Supervised and Unsupervised Machine Learning","author":"Kim S.","year":"2015"},{"key":"bibr14-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-1184-5"},{"key":"bibr15-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1111\/biom.12540"},{"key":"bibr16-1177932218759292","volume-title":"Introduction to Machine Learning","author":"Alpaydin E.","year":"2010"},{"key":"bibr17-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2013.0043"},{"key":"bibr18-1177932218759292","doi-asserted-by":"publisher","DOI":"10.2202\/1544-6115.1540"},{"key":"bibr19-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-0912-1"},{"key":"bibr20-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1039\/c3mb70327d"},{"key":"bibr21-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu025"},{"key":"bibr22-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0073074"},{"key":"bibr23-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/s12918-015-0207-6"},{"key":"bibr24-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq182"},{"key":"bibr25-1177932218759292","first-page":"91","volume":"11","author":"Martin A","year":"2015","journal-title":"BMC Syst Biol"},{"key":"bibr26-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/biostatistics\/kxs016"},{"key":"bibr27-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-459"},{"key":"bibr28-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-7-134"},{"key":"bibr29-1177932218759292","volume-title":"Paper presented at: Statistical Methods for Omics Data Integration and Analysis","author":"Acharjee A"},{"key":"bibr30-1177932218759292","doi-asserted-by":"publisher","DOI":"10.2202\/1544-6115.1390"},{"key":"bibr31-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1002\/cem.1359"},{"key":"bibr32-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/s12918-016-0256-5"},{"key":"bibr33-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/s12918-016-0260-9"},{"key":"bibr34-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1016\/j.artmed.2011.09.003"},{"key":"bibr35-1177932218759292","volume-title":"Paper presented at: Statistical Methods for Omics Data Integration and Analysis","author":"Gomez-Cabrero D"},{"key":"bibr36-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr499"},{"key":"bibr37-1177932218759292","first-page":"603","volume":"17","author":"Kannan L","year":"2016","journal-title":"Bioinformatics"},{"key":"bibr38-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr019"},{"key":"bibr39-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-10-r105"},{"key":"bibr40-1177932218759292","unstructured":"iClusterPlus: integrative clustering of type genomic data [computer program]. R package version 1.12.1; 2016. https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/iClusterPlus.html"},{"key":"bibr41-1177932218759292","unstructured":"STATegRa: classes and methods for multi-omics data integration [computer program]. R package version 1.10.0; 2017. http:\/\/bioconductor.org\/packages\/release\/bioc\/html\/STATegRa.html"},{"key":"bibr42-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbn058"},{"key":"bibr43-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts595"},{"key":"bibr44-1177932218759292","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2010.11.013"},{"key":"bibr45-1177932218759292","doi-asserted-by":"publisher","DOI":"10.18547\/gcb.2016.vol2.iss1.e32"}],"container-title":["Bioinformatics and Biology Insights"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/1177932218759292","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1177\/1177932218759292","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/1177932218759292","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T12:55:07Z","timestamp":1777380907000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.1177\/1177932218759292"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,1,1]]},"references-count":69,"alternative-id":["10.1177\/1177932218759292"],"URL":"https:\/\/doi.org\/10.1177\/1177932218759292","relation":{},"ISSN":["1177-9322","1177-9322"],"issn-type":[{"value":"1177-9322","type":"print"},{"value":"1177-9322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,1,1]]},"article-number":"1177932218759292"}}