{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T20:02:41Z","timestamp":1778097761456,"version":"3.51.4"},"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2013,3,7]],"date-time":"2013-03-07T00:00:00Z","timestamp":1362614400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002956","type":"journal-article","created":{"date-parts":[[2013,3,7]],"date-time":"2013-03-07T21:55:13Z","timestamp":1362693313000},"page":"e1002956","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":24,"title":["Integrative Analysis Using Module-Guided Random Forests Reveals Correlated Genetic Factors Related to Mouse Weight"],"prefix":"10.1371","volume":"9","author":[{"given":"Zheng","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weixiong","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2013,3,7]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/nature05911","article-title":"Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls","volume":"447","year":"2007","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1126\/science.1141634","article-title":"A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity","volume":"316","author":"TM Frayling","year":"2007","journal-title":"Science"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1038\/nrg2344","article-title":"Genome-wide association studies for complex traits: consensus, uncertainty and challenges","volume":"9","author":"MI McCarthy","year":"2008","journal-title":"Nature reviews Genetics"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1093\/bioinformatics\/btp713","article-title":"Bioinformatics challenges for genome-wide association studies","volume":"26","author":"JH Moore","year":"2010","journal-title":"Bioinformatics"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"e1000337","DOI":"10.1371\/journal.pgen.1000337","article-title":"Interpretation of genetic association studies: markers with replicated highly significant odds ratios may be poor classifiers","volume":"5","author":"J Jakobsdottir","year":"2009","journal-title":"PLoS Genetics"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"4356","DOI":"10.1093\/bioinformatics\/bti724","article-title":"Regularized ROC method for disease classification and biomarker selection with microarray data","volume":"21","author":"S Ma","year":"2005","journal-title":"Bioinformatics"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"2394","DOI":"10.1093\/bioinformatics\/bti319","article-title":"Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data","volume":"21","author":"KY Yeung","year":"2005","journal-title":"Bioinformatics"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1023\/A:1012487302797","article-title":"Gene Selection for Cancer Classification using Support Vector Machines","volume":"46","author":"I Guyon","year":"2002","journal-title":"Machine Learning"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.1038\/ng1619","article-title":"Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits","volume":"37","author":"M Mehrabian","year":"2005","journal-title":"Nature Genetics"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1038\/ng1589","article-title":"An integrative genomics approach to infer causal associations between gene expression and disease","volume":"37","author":"EE Schadt","year":"2005","journal-title":"Nature Genetics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1038\/nrg1964","article-title":"Genetics of global gene expression","volume":"7","author":"MV Rockman","year":"2006","journal-title":"Nature Reviews Genetics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e130","DOI":"10.1371\/journal.pgen.0020130","article-title":"Integrating genetic and network analysis to characterize genes related to mouse weight","volume":"2","author":"A Ghazalpour","year":"2006","journal-title":"PLoS Genetics"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"e69","DOI":"10.1371\/journal.pcbi.0030069","article-title":"Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations","volume":"3","author":"J Zhu","year":"2007","journal-title":"PLoS Computational Biology"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/j.ajhg.2009.03.011","article-title":"Genetic control of human brain transcript expression in Alzheimer disease","volume":"84","author":"JA Webster","year":"2009","journal-title":"American Journal of Human Genetics"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"e6907","DOI":"10.1371\/journal.pone.0006907","article-title":"Using expression and genotype to predict drug response in yeast","volume":"4","author":"DM Ruderfer","year":"2009","journal-title":"PloS One"},{"key":"ref16","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":"H Zou","year":"2005","journal-title":"Journal of the Royal Statistical Society - Series B: Statistical Methodology"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1038\/msb.2009.69","article-title":"Harnessing gene expression to identify the genetic basis of drug resistance","volume":"5","author":"B-J Chen","year":"2009","journal-title":"Molecular Systems Biology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random Forests","volume":"45","author":"L Breiman","year":"2001","journal-title":"Machine Learning"},{"key":"ref19","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1031","article-title":"Relating HIV-1 sequence variation to replication capacity via trees and forests","volume":"3","author":"MR Segal","year":"2004","journal-title":"Statistical Applications in Genetics and Molecular Biology"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1471-2105-7-3","article-title":"Gene selection and classification of microarray data using random forest","volume":"7","author":"R D\u00edaz-Uriarte","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"S65","DOI":"10.1186\/1471-2105-10-S1-S65","article-title":"A random forest approach to the detection of epistatic interactions in case-control studies","volume":"10 Suppl 1","author":"R Jiang","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1471-2156-11-49","article-title":"An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings","volume":"11","author":"BA Goldstein","year":"2010","journal-title":"BMC Genetics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"e1002180","DOI":"10.1371\/journal.pcbi.1002180","article-title":"Protein Networks as Logic Functions in Development and Cancer","volume":"7","author":"J Dutkowski","year":"2011","journal-title":"PLoS Computational Biology"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/1471-2105-8-25","article-title":"Bias in random forest variable importance measures: illustrations, sources and a solution","volume":"8","author":"C Strobl","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"32","DOI":"10.2202\/1544-6115.1691","article-title":"Random Forests for Genetic Association Studies","volume":"10","author":"BA Goldstein","year":"2011","journal-title":"Statistical Applications in Genetics and Molecular Biology"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"2010","DOI":"10.1093\/bioinformatics\/btn356","article-title":"Enriched random forests","volume":"24","author":"D Amaratunga","year":"2008","journal-title":"Bioinformatics"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"16104","DOI":"10.1103\/PhysRevE.77.016104","article-title":"Identifying network communities with a high resolution","volume":"77","author":"J Ruan","year":"2008","journal-title":"Physical Review E"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1186\/1752-0509-4-136","article-title":"Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks","volume":"4","author":"M Ray","year":"2010","journal-title":"BMC Systems Biology"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1752-0509-4-8","article-title":"A general co-expression network-based approach to gene expression analysis: comparison and applications","volume":"4","author":"J Ruan","year":"2010","journal-title":"BMC Systems Biology"},{"key":"ref30","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":"M Yuan","year":"2006","journal-title":"Journal of the Royal Statistical Society - Series B: Statistical Methodology"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/j.ajhg.2009.03.011","article-title":"Genetic control of human brain transcript expression in Alzheimer disease","volume":"84","author":"JA Webster","year":"2009","journal-title":"The American Journal of Human Genetics"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"Article17","DOI":"10.2202\/1544-6115.1128","article-title":"A general framework for weighted gene co-expression network analysis","volume":"4","author":"B Zhang","year":"2005","journal-title":"Statistical Applications in Genetics and Molecular Biology"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1371\/journal.pgen.0020015","article-title":"Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity","volume":"2","author":"S Wang","year":"2006","journal-title":"PLoS Genetics"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1186\/1471-2164-11-713","article-title":"Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL\/6J\u00d7TALLYHO\/JngJ) F2 mice","volume":"11","author":"TP Stewart","year":"2010","journal-title":"BMC Genomics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"285","DOI":"10.2337\/db06-0436","article-title":"IGF-binding protein-2 protects against the development of obesity and insulin resistance","volume":"56","author":"SB Wheatcroft","year":"2007","journal-title":"Diabetes"},{"key":"ref36","first-page":"9","article-title":"Effects of adiponectin on the osteosarcoma cell line Saos-2","volume":"19","author":"EL Pacheco-Pantoja","year":"2009","journal-title":"Endocrine Abstracts"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"R148","DOI":"10.1186\/gb-2008-9-10-r148","article-title":"Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases","volume":"9","author":"M Ray","year":"2008","journal-title":"Genome Biology"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1093\/biostatistics\/kxl002","article-title":"Averaged gene expressions for regression","volume":"8","author":"MY Park","year":"2007","journal-title":"Biostatistics"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1986","DOI":"10.1093\/bioinformatics\/btr300","article-title":"Classification with correlated features: unreliability of feature ranking and solutions","volume":"27","author":"L Tolosi","year":"2011","journal-title":"Bioinformatics"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/1471-2105-10-78","article-title":"Performance of random forest when SNPs are in linkage disequilibrium","volume":"10","author":"YA Meng","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/1471-2105-11-110","article-title":"The behaviour of random forest permutation-based variable importance measures under predictor correlation","volume":"11","author":"KK Nicodemus","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1186\/1471-2105-9-307","article-title":"Conditional variable importance for random forests","volume":"9","author":"C Strobl","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"e62","DOI":"10.1093\/nar\/gkr064","article-title":"Ranking causal variants and associated regions in genome-wide association studies by the support vector machine and random forest","volume":"39","author":"U Roshan","year":"2011","journal-title":"Nucleic Acids Research"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"026113","DOI":"10.1103\/PhysRevE.69.026113","article-title":"Finding and evaluating community structure in networks","volume":"69","author":"M Newman","year":"2004","journal-title":"Physical Review E"},{"key":"ref45","unstructured":"Breiman L, Friedman J, Stone CJ, Olshen RA (1984) Classification and Regression Trees. New York, NY, USA: Chapman & Hall\/CRC."},{"key":"ref46","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nature Genetics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002956","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,7,23]],"date-time":"2020-07-23T11:00:20Z","timestamp":1595502020000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002956"}},"subtitle":[],"editor":[{"given":"Frederick P.","family":"Roth","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2013,3,7]]},"references-count":46,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2013,3,7]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002956","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,3,7]]}}}