{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T05:10:27Z","timestamp":1784265027087,"version":"3.55.0"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Epistasis or gene\u2013gene interaction has gained increasing attention in studies of complex diseases. Its presence as an ubiquitous component of genetic architecture of common human diseases has been contemplated. However, the detection of gene\u2013gene interaction is difficult due to combinatorial explosion.<\/jats:p><jats:p>Results: We present a novel feature selection method incorporating variable interaction. Three gene expression datasets are analyzed to illustrate our method, although it can also be applied to other types of high-dimensional data. The quality of variables selected is evaluated in two ways: first by classification error rates, then by functional relevance assessed using biological knowledge. We show that the classification error rates can be significantly reduced by considering interactions. Secondly, a sizable portion of genes identified by our method for breast cancer metastasis overlaps with those reported in gene-to-system breast cancer (G2SBC) database as disease associated and some of them have interesting biological implication. In summary, interaction-based methods may lead to substantial gain in biological insights as well as more accurate prediction.<\/jats:p><jats:p>Contact: \u00a0imichu@ust.hk; slo@stat.columnbia.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at the Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts531","type":"journal-article","created":{"date-parts":[[2012,9,4]],"date-time":"2012-09-04T00:49:26Z","timestamp":1346719766000},"page":"2834-2842","source":"Crossref","is-referenced-by-count":42,"title":["Interaction-based feature selection and classification for high-dimensional biological data"],"prefix":"10.1093","volume":"28","author":[{"given":"Haitian","family":"Wang","sequence":"first","affiliation":[{"name":"1 Department of ISOM, HKUST, Clear Water Bay, Kowloon, 2Division of Biostatistics, School of Public Health and Primary Care, CUHK, Shatin, Hong Kong and 3Department of Statistics, Columbia University, New York, NY 10027, USA"},{"name":"1 Department of ISOM, HKUST, Clear Water Bay, Kowloon, 2Division of Biostatistics, School of Public Health and Primary Care, CUHK, Shatin, Hong Kong and 3Department of Statistics, Columbia University, New York, NY 10027, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaw-Hwa","family":"Lo","sequence":"additional","affiliation":[{"name":"1 Department of ISOM, HKUST, Clear Water Bay, Kowloon, 2Division of Biostatistics, School of Public Health and Primary Care, CUHK, Shatin, Hong Kong and 3Department of Statistics, Columbia University, New York, NY 10027, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tian","family":"Zheng","sequence":"additional","affiliation":[{"name":"1 Department of ISOM, HKUST, Clear Water Bay, Kowloon, 2Division of Biostatistics, School of Public Health and Primary Care, CUHK, Shatin, Hong Kong and 3Department of Statistics, Columbia University, New York, NY 10027, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Inchi","family":"Hu","sequence":"additional","affiliation":[{"name":"1 Department of ISOM, HKUST, Clear Water Bay, Kowloon, 2Division of Biostatistics, School of Public Health and Primary Care, CUHK, Shatin, Hong Kong and 3Department of Statistics, Columbia University, New York, NY 10027, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,9,3]]},"reference":[{"key":"2023012513145844500_bts531-B1","volume-title":"An Introduction to Categorical Data Analysis","author":"Agresti","year":"1996"},{"key":"2023012513145844500_bts531-B2","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1007\/s12253-010-9355-6","article-title":"Prognostic significance of carbonic anhydrase IX (CA-IX), endoglin (CD105) and 8-hydroxy-2\u2032-deoxyguanosine (8-OHdG) in breast cancer patients","volume":"17","author":"Beketic-Oreskovic","year":"2011","journal-title":"Pathol. Oncol. Res."},{"key":"2023012513145844500_bts531-B3","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate-a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"JRSS B"},{"key":"2023012513145844500_bts531-B4","first-page":"532","article-title":"Random forests","volume":"45","author":"Breiman","year":"2001","journal-title":"Mach. Learn."},{"key":"2023012513145844500_bts531-B5","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/nrg1407","article-title":"Epistasis: too often neglected in complex trait studies","volume":"5","author":"Carlborg","year":"2004","journal-title":"Nat. Rev. Genet."},{"key":"2023012513145844500_bts531-B6","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1214\/09-AOAS265","article-title":"Discovering influential variables: a method of partitions","volume":"3","author":"Chernoff","year":"2009","journal-title":"Ann. Appl. Stat."},{"key":"2023012513145844500_bts531-B7","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1038\/nrg2579","article-title":"Detecting gene\u2013gene interactions that underlies human diseases","volume":"10","author":"Cordell","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"2023012513145844500_bts531-B8","doi-asserted-by":"crossref","first-page":"131","DOI":"10.3233\/IDA-1997-1302","article-title":"Feature selection for classification","volume":"1","author":"Dash","year":"1997","journal-title":"Intel. Data Anal."},{"key":"2023012513145844500_bts531-B9","first-page":"1","article-title":"Ensemble methods in machine learning","volume-title":"First International Workshop on Multiple Classifier Systems, Lecture Notes in Computer Science.(.)","author":"Dietterich","year":"2000"},{"key":"2023012513145844500_bts531-B10","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1198\/016214501753382129","article-title":"Empirical Bayes analysis of a microarray experiment","volume":"96","author":"Efron","year":"2001","journal-title":"JASA"},{"key":"2023012513145844500_bts531-B11","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1111\/j.1467-9868.2008.00674.x","article-title":"Sure independence screening for ultrahigh dimensional feature space (with discussion)","volume":"70","author":"Fan","year":"2008","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"2023012513145844500_bts531-B12","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1006\/jcss.1997.1504","article-title":"A decision-theoretic generalization of online learning and an application to boosting","volume":"55","author":"Freund","year":"1997","journal-title":"J. Comput. Sys. Sci."},{"key":"2023012513145844500_bts531-B13","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"},{"key":"2023012513145844500_bts531-B14","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1023\/A:1012487302797","article-title":"Gene selection for cancer classification using support vector machine","volume":"46","author":"Guyon","year":"2002","journal-title":"Mach. Learn."},{"key":"2023012513145844500_bts531-B15","first-page":"1157","article-title":"An introduction to variable and feature selection","volume":"3","author":"Guyon","year":"2003","journal-title":"JMLR"},{"key":"2023012513145844500_bts531-B16","volume-title":"The Theory of Coverage Process","author":"Hall","year":"1988"},{"key":"2023012513145844500_bts531-B17","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1126\/science.1203801","article-title":"Negative epistasis between beneficial mutations in an evolving bacterial population","volume":"332","author":"Khan","year":"2011","journal-title":"Science"},{"key":"2023012513145844500_bts531-B18","first-page":"472","article-title":"Structures and assumptions: strategies to harness gene x gene and gene x environment interactions in GWAS","volume":"24","author":"Kooperberg","year":"2010","journal-title":"Stat. Sci."},{"key":"2023012513145844500_bts531-B19","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1109\/TKDE.2005.66","article-title":"Toward integrating feature selection algorithms for classification and clustering","volume":"17","author":"Liu","year":"2005","journal-title":"IEEE Tran. Knowl Data Eng."},{"key":"2023012513145844500_bts531-B20","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1159\/000066194","article-title":"Backward haplotype transmission association algorithm\u2014a fast multiple-marker screening method","volume":"53","author":"Lo","year":"2002","journal-title":"Hum. Her."},{"key":"2023012513145844500_bts531-B21","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/j.ajhg.2009.08.006","article-title":"Epistasis and its implication for personal genetics","volume":"853","author":"Moore","year":"2009","journal-title":"Am. J. Hum. Gen."},{"key":"2023012513145844500_bts531-B37","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1038\/35021093","article-title":"Molecular portraits of human breast tumours","volume":"406","author":"Perou","year":"2000","journal-title":"Nature"},{"key":"2023012513145844500_bts531-B22","first-page":"1279","article-title":"GLUT1 and CAIX expression profiles in breast cancer correlate with adverse prognostic factors and MCT1 overexpression","volume":"26","author":"Pinheiro","year":"2011","journal-title":"Histol. Histopathol."},{"key":"2023012513145844500_bts531-B23","doi-asserted-by":"crossref","first-page":"2507","DOI":"10.1093\/bioinformatics\/btm344","article-title":"A review of feature selection techniques in bioinformatics","volume":"23","author":"Saeys","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012513145844500_bts531-B24","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1093\/biostatistics\/kxm024","article-title":"Identification of SNP interactions using logic regression","volume":"9","author":"Schwender","year":"2008","journal-title":"Biostatistics"},{"key":"2023012513145844500_bts531-B25","doi-asserted-by":"crossref","first-page":"19910","DOI":"10.1073\/pnas.0810388105","article-title":"Genetic architecture of complex traits: large phenotypic effects and pervasive epistasis","volume":"105","author":"Shao","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012513145844500_bts531-B26","doi-asserted-by":"crossref","first-page":"10393","DOI":"10.1073\/pnas.1732912100","article-title":"Breast cancer classification and prognosis based on gene expression profiles from a population-based study","volume":"100","author":"Sotiriou","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012513145844500_bts531-B27","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","article-title":"Regression shrinkage and selection via the lasso","volume":"58","author":"Tibshirani","year":"1996","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"2023012513145844500_bts531-B28","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1000","article-title":"Pre-validation and inference in microarray","volume":"1","author":"Tibshirani","year":"2002","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"2023012513145844500_bts531-B29","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1038\/415530a","article-title":"Gene expression profiling predicts clinical outcome of breast cancer","volume":"415","author":"van\u2019t Veer","year":"2002","journal-title":"Nature"},{"key":"2023012513145844500_bts531-B30","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1111\/j.1467-9868.2005.00532.x","article-title":"Model selection and estimation in regression with grouped variables","volume":"68","author":"Yuan","year":"2006","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"2023012513145844500_bts531-B31","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1093\/hmg\/11.4.389","article-title":"KRIT1 association with the integrin-binding protein ICAP-1: a new direction in the elucidation of cerebral cavernous malformations (CCM1) pathogenesis","volume":"11","author":"Zawistowski","year":"2002","journal-title":"Hum. Mol. Genet."},{"key":"2023012513145844500_bts531-B32","doi-asserted-by":"crossref","first-page":"2953","DOI":"10.1093\/hmg\/10.25.2953","article-title":"Interaction between krit1 and icap1alpha infers perturbation of integrin beta1-mediated angiogenesis in the pathogenesis of cerebral cavernous malformation","volume":"10","author":"Zhang","year":"2001","journal-title":"Hum. Mol. Genet."},{"key":"2023012513145844500_bts531-B33","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1093\/bioinformatics\/bti736","article-title":"Gene selection using support vector machine with non-convex penalty","volume":"22","author":"Zhang","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012513145844500_bts531-B34","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.jspi.2007.06.003","article-title":"On selection bias with prediction rules formed from gene expression data","volume":"138","author":"Zhu","year":"2008","journal-title":"J. Stat. Plann. Infer."},{"key":"2023012513145844500_bts531-B35","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1111\/j.1467-9868.2005.00503.x","article-title":"Regularization and variable selection via the elastic net","volume":"67","author":"Zou","year":"2005","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"2023012513145844500_bts531-B36","article-title":"The mystery of missing heritability: genetic interactions create phantom heritability","author":"Zuk","year":"2011","journal-title":"Proc. Natl Acad. Sci. USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/21\/2834\/48872422\/bioinformatics_28_21_2834.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/21\/2834\/48872422\/bioinformatics_28_21_2834.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,28]],"date-time":"2024-04-28T22:19:18Z","timestamp":1714342758000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/21\/2834\/236824"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,9,3]]},"references-count":37,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2012,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts531","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,11,1]]},"published":{"date-parts":[[2012,9,3]]}}}