{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T22:18:27Z","timestamp":1784845107278,"version":"3.55.0"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1423,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Analyzing data from multi-platform genomics experiments combined with patients\u2019 clinical outcomes helps us understand the complex biological processes that characterize a disease, as well as how these processes relate to the development of the disease. Current data integration approaches are limited in that they do not consider the fundamental biological relationships that exist among the data obtained from different platforms.<\/jats:p><jats:p>Statistical Model: We propose an integrative Bayesian analysis of genomics data (iBAG) framework for identifying important genes\/biomarkers that are associated with clinical outcome. This framework uses hierarchical modeling to combine the data obtained from multiple platforms into one model.<\/jats:p><jats:p>Results: We assess the performance of our methods using several synthetic and real examples. Simulations show our integrative methods to have higher power to detect disease-related genes than non-integrative methods. Using the Cancer Genome Atlas glioblastoma dataset, we apply the iBAG model to integrate gene expression and methylation data to study their associations with patient survival. Our proposed method discovers multiple methylation-regulated genes that are related to patient survival, most of which have important biological functions in other diseases but have not been previously studied in glioblastoma.<\/jats:p><jats:p>Availability: \u00a0http:\/\/odin.mdacc.tmc.edu\/\u223cvbaladan\/.<\/jats:p><jats:p>Contact: \u00a0veera@mdanderson.org<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts655","type":"journal-article","created":{"date-parts":[[2012,11,10]],"date-time":"2012-11-10T04:30:01Z","timestamp":1352521801000},"page":"149-159","source":"Crossref","is-referenced-by-count":123,"title":["iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data"],"prefix":"10.1093","volume":"29","author":[{"given":"Wenting","family":"Wang","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Bioinformatics and Computational Biology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veerabhadran","family":"Baladandayuthapani","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Bioinformatics and Computational Biology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey S.","family":"Morris","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Bioinformatics and Computational Biology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bradley M.","family":"Broom","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Bioinformatics and Computational Biology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ganiraju","family":"Manyam","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Bioinformatics and Computational Biology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kim-Anh","family":"Do","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Bioinformatics and Computational Biology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,11,9]]},"reference":[{"key":"2023012810154708300_bts655-B1","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1080\/01621459.1993.10476321","article-title":"Bayesian analysis of binary and polychotomous response data","volume":"88","author":"Albert","year":"1993","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012810154708300_bts655-B2","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1046\/j.1528-1157.2003.22103.x","article-title":"Overexpression of the human major vault protein in gangliogliomas","volume":"44","author":"Aronica","year":"2003","journal-title":"Epilepsia"},{"key":"2023012810154708300_bts655-B3","doi-asserted-by":"crossref","first-page":"1238","DOI":"10.1038\/ng.465","article-title":"SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas","volume":"41","author":"Bass","year":"2009","journal-title":"Nat. Genet."},{"key":"2023012810154708300_bts655-B4","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":"J. Roy. Stat. Soc. B"},{"key":"2023012810154708300_bts655-B5","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1093\/bioinformatics\/btq660","article-title":"Bayesian ensemble methods for survival prediction in gene expression data","volume":"27","author":"Bonato","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810154708300_bts655-B6","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1080\/00031305.1992.10475878","article-title":"Explaining the Gibbs sampler","volume":"46","author":"Casella","year":"1992","journal-title":"Am. Stat."},{"key":"2023012810154708300_bts655-B7","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1101\/gad.2017311","article-title":"Making sense of cancer genomic data","volume":"25","author":"Chin","year":"2011","journal-title":"Genes Dev."},{"key":"2023012810154708300_bts655-B8","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/gm39","article-title":"A kernel-based integration of genome-wide data for clinical decision support","volume":"1","author":"Daemen","year":"2009","journal-title":"Genome Med."},{"key":"2023012810154708300_bts655-B9","doi-asserted-by":"crossref","first-page":"P3","DOI":"10.1186\/gb-2003-4-5-p3","article-title":"DAVID: database for annotation, visualization, and integrated discovery","volume":"4","author":"Dennis","year":"2003","journal-title":"Genome Biol."},{"key":"2023012810154708300_bts655-B10","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/1471-2164-10-32","article-title":"Simultaneous analysis of distinct Omics data sets with integration of biological knowledge: multiple factor analysis approach","volume":"10","author":"de Tayrac","year":"2009","journal-title":"BMC Genomics"},{"key":"2023012810154708300_bts655-B11","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1214\/009053604000000067","article-title":"Least angle regression","volume":"32","author":"Efron","year":"2004","journal-title":"Ann. Statist."},{"key":"2023012810154708300_bts655-B12","doi-asserted-by":"crossref","first-page":"2275","DOI":"10.3109\/10428194.2010.528093","article-title":"Analysis of genome-wide methylation and gene expression induced by 5-aza-2\u2019-deoxycytidine identifies BCL2L10 as a frequent methylation target in acute myeloid leukemia","volume":"51","author":"Fabiani","year":"2010","journal-title":"Leuk. Lymphoma."},{"key":"2023012810154708300_bts655-B13","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1186\/1471-2407-6-96","article-title":"Breast tumor copy number aberration phenotypes and genomic instability","volume":"6","author":"Fridlyand","year":"2006","journal-title":"BMC Cancer"},{"key":"2023012810154708300_bts655-B14","doi-asserted-by":"crossref","first-page":"2613","DOI":"10.4161\/cc.5.22.3498","article-title":"Integration of HapMap-based SNP pattern analysis and gene expression profiling reveals common SNP profiles for cancer therapy outcome predictor genes","volume":"5","author":"Glinsky","year":"2006","journal-title":"Cell Cycle"},{"key":"2023012810154708300_bts655-B15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.4061\/2009\/869093","article-title":"Data integration in genetics and genomics: methods and challenges","volume":"1","author":"Hamid","year":"2009","journal-title":"Hum. Genomics Proteomics"},{"key":"2023012810154708300_bts655-B16","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1038\/sj.bjc.6605635","article-title":"Clinical responses observed with imatinib or sorafenib in melanoma patients expressing mutations in KIT","volume":"102","author":"Handolias","year":"2010","journal-title":"Br. J. Cancer"},{"key":"2023012810154708300_bts655-B17","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-3462-1","volume-title":"Regression Modeling Strategies, with Applications to Linear Models, Survival Analysis and Logistic Regression","author":"Harrel","year":"2001"},{"key":"2023012810154708300_bts655-B18","doi-asserted-by":"crossref","first-page":"e1000130","DOI":"10.1371\/journal.pgen.1000130","article-title":"Simultaneous analysis of all SNPs in genome-wide and re-sequencing studies","volume":"4","author":"Hoggart","year":"2008","journal-title":"PLoS Genet."},{"key":"2023012810154708300_bts655-B19","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1038\/nature08987","article-title":"International network of cancer genome projects","volume":"464","author":"Hudson","year":"2010","journal-title":"Nature"},{"key":"2023012810154708300_bts655-B20","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1038\/labinvest.3700707","article-title":"DNA methylation profiles of gastric carcinoma characterized by quantitative DNA methylation analysis","volume":"88","author":"Kang","year":"2008","journal-title":"Lab Invest."},{"key":"2023012810154708300_bts655-B21","doi-asserted-by":"crossref","DOI":"10.1109\/BIBMW.2010.5703810","article-title":"Relational database index choices for genome annotation data","volume-title":"Bioinformatics and Biomedicine Workshops (BIBMW)","author":"Karpenko","year":"2010"},{"key":"2023012810154708300_bts655-B22","doi-asserted-by":"crossref","first-page":"2626","DOI":"10.1093\/bioinformatics\/bth294","article-title":"A statistical framework for genomic data fusion","volume":"20","author":"Lanckriet","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012810154708300_bts655-B23","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1093\/bioinformatics\/btq688","article-title":"The Bayesian lasso for genome-wide association studies","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810154708300_bts655-B24","doi-asserted-by":"crossref","first-page":"2219","DOI":"10.1210\/en.2007-1320","article-title":"Transcriptional activation of signal transducer and activator of transcription (STAT) 3 and STAT5B partially mediate homeobox A1-stimulated oncogenic transformation of the immortalized human mammary epithelial cell","volume":"149","author":"Mohankumar","year":"2008","journal-title":"Endocrinology"},{"key":"2023012810154708300_bts655-B25","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1111\/j.1541-0420.2007.00895.x","article-title":"Bayesian analysis of mass spectrometry data using wavelet-based functional mixed models","volume":"64","author":"Morris","year":"2008","journal-title":"Biometrics"},{"key":"2023012810154708300_bts655-B47","doi-asserted-by":"crossref","first-page":"3074","DOI":"10.1158\/0008-5472.CAN-06-2366","article-title":"Amplification of MDS1\/EVI1 and EVI1, located in the 3q26.2 amplicon, is associated with favorable patient prognosis in ovarian cancer","volume":"67","author":"Nanjundan","year":"2007","journal-title":"Cancer Res."},{"key":"2023012810154708300_bts655-B26","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1093\/biostatistics\/5.2.155","article-title":"Detecting differential gene expression with a semiparametric hierarchical mixture method","volume":"5","author":"Newton","year":"2004","journal-title":"Biostatistics"},{"key":"2023012810154708300_bts655-B27","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1016\/j.ccr.2010.03.017","article-title":"The cancer genome atlas research network, identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma","volume":"17","author":"Noushmehr","year":"2010","journal-title":"Cancer Cell"},{"key":"2023012810154708300_bts655-B28","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1198\/016214508000000337","article-title":"The Bayesian lasso","volume":"103","author":"Park","year":"2008","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012810154708300_bts655-B29","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1007\/s00428-010-1013-6","article-title":"Promoter CpG island hypermethylation during breast cancer progression","volume":"458","author":"Park","year":"2011","journal-title":"Virchows Arch."},{"key":"2023012810154708300_bts655-B30","first-page":"13","article-title":"Biological rationale for HER2\/neu (c-erbB2) as a target for monoclonal antibody therapy","volume":"5","author":"Pegram","year":"2000","journal-title":"Semin. Oncol."},{"key":"2023012810154708300_bts655-B31","first-page":"53","article-title":"Regularized multivariate regression for identifying master predictors with application to integrative genomics study of breast cancer","volume":"4","author":"Peng","year":"2010","journal-title":"Ann. Statist."},{"key":"2023012810154708300_bts655-B32","doi-asserted-by":"crossref","first-page":"369","DOI":"10.4137\/CIN.S633","article-title":"An integrative analysis of microRNA and mRNA expression-a case study","volume":"6","author":"Qin","year":"2008","journal-title":"Cancer Inform."},{"key":"2023012810154708300_bts655-B33","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1038\/nature08109","article-title":"GOLPH3 modulates mTOR signalling and rapamycin sensitivity in cancer","volume":"459","author":"Scott","year":"2009","journal-title":"Nature"},{"key":"2023012810154708300_bts655-B34","doi-asserted-by":"crossref","first-page":"e21443","DOI":"10.1371\/journal.pone.0021443","article-title":"DNA methylation changes in atypical adenomatous hyperplasia, adenocarcinoma in situ, and lung adenocarcinoma","volume":"6","author":"Selamat","year":"2011","journal-title":"PLoS One"},{"key":"2023012810154708300_bts655-B35","doi-asserted-by":"crossref","first-page":"9440","DOI":"10.1073\/pnas.1530509100","article-title":"Statistical significance for genome-wide experiments","volume":"100","author":"Storey","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012810154708300_bts655-B36","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1080\/01621459.1987.10478458","article-title":"The calculation of posterior distributions by data augmentation (with discussion)","volume":"82","author":"Tanner","year":"1987","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012810154708300_bts655-B37","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1186\/1752-0509-5-99","article-title":"Integrative network analysis reveals active microRNAs and their functions in gastric cancer","volume":"5","author":"Tseng","year":"2011","journal-title":"BMC Syst. Biol."},{"key":"2023012810154708300_bts655-B38","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. Roy. Stat. Soc. B"},{"key":"2023012810154708300_bts655-B39","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1038\/sj.onc.1210661","article-title":"Novel risk stratification of patients with neuroblastoma by genomic signature, which is independent of molecular signature","volume":"27","author":"Tomioka","year":"2008","journal-title":"Oncogene"},{"key":"2023012810154708300_bts655-B40","doi-asserted-by":"crossref","first-page":"1590","DOI":"10.1016\/j.csda.2008.05.021","article-title":"Survival prediction using gene expression data: a review and comparison","volume":"53","author":"van Wieringen","year":"2009","journal-title":"Comput. Stat. Data Anal."},{"key":"2023012810154708300_bts655-B41","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/1471-2105-13-80","article-title":"Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses","volume":"13","author":"van Wieringen","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023012810154708300_bts655-B42","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.ccr.2009.12.020","article-title":"Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1","volume":"17","author":"Verhaak","year":"2010","journal-title":"Cancer Cell"},{"key":"2023012810154708300_bts655-B43","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1016\/0168-9525(93)90209-Z","article-title":"The multistep nature of cancer","volume":"9","author":"Vogelstein","year":"1993","journal-title":"Trends Genet."},{"key":"2023012810154708300_bts655-B44","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1016\/j.ccr.2004.11.004","article-title":"Somatic alterations in the human cancer genome","volume":"6","author":"Weir","year":"2004","journal-title":"Cancer Cell"},{"key":"2023012810154708300_bts655-B45","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1093\/bfgp\/ell019","article-title":"Data merging for integrated microarray and proteomic analysis","volume":"5","author":"Waters","year":"2006","journal-title":"Brief Funct. Genomic Proteomic."},{"key":"2023012810154708300_bts655-B46","doi-asserted-by":"crossref","first-page":"28","DOI":"10.2202\/1544-6115.1470","article-title":"Extensions of sparse canonical correlation analysis, with applications to genomic data","volume":"8","author":"Witten","year":"2009","journal-title":"Stat. Appl. Genet. Mol. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/2\/149\/48894449\/bioinformatics_29_2_149.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/2\/149\/48894449\/bioinformatics_29_2_149.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T07:22:07Z","timestamp":1714548127000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/2\/149\/201269"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,11,9]]},"references-count":47,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2013,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts655","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,1,15]]},"published":{"date-parts":[[2012,11,9]]}}}