{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T16:19:09Z","timestamp":1779898749646,"version":"3.53.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"22","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01GM109068"],"award-info":[{"award-number":["R01GM109068"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01MH104680"],"award-info":[{"award-number":["R01MH104680"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01MH107354"],"award-info":[{"award-number":["R01MH107354"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["P20GM103472"],"award-info":[{"award-number":["P20GM103472"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Science Foundation","award":["#1539067"],"award-info":[{"award-number":["#1539067"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,11,15]]},"abstract":"<jats:p>Motivation: Imaging genetics combines brain imaging and genetic information to identify the relationships between genetic variants and brain activities. When the data samples belong to different classes (e.g. disease status), the relationships may exhibit class-specific patterns that can be used to facilitate the understanding of a disease. Conventional approaches often perform separate analysis on each class and report the differences, but ignore important shared patterns.<\/jats:p>\n               <jats:p>Results: In this paper, we develop a multivariate method to analyze the differential dependency across multiple classes. We propose a joint sparse canonical correlation analysis method, which uses a generalized fused lasso penalty to jointly estimate multiple pairs of canonical vectors with both shared and class-specific patterns. Using a data fusion approach, the method is able to detect differentially correlated modules effectively and efficiently. The results from simulation studies demonstrate its higher accuracy in discovering both common and differential canonical correlations compared to conventional sparse CCA. Using a schizophrenia dataset with 92 cases and 116 controls including a single nucleotide polymorphism (SNP) array and functional magnetic resonance imaging data, the proposed method reveals a set of distinct SNP-voxel interaction modules for the schizophrenia patients, which are verified to be both statistically and biologically significant.<\/jats:p>\n               <jats:p>Availability and Implementation: The Matlab code is available at https:\/\/sites.google.com\/site\/jianfang86\/JSCCA.<\/jats:p>\n               <jats:p>Contact: \u00a0wyp@tulane.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw485","type":"journal-article","created":{"date-parts":[[2016,7,28]],"date-time":"2016-07-28T02:29:14Z","timestamp":1469672954000},"page":"3480-3488","source":"Crossref","is-referenced-by-count":71,"title":["Joint sparse canonical correlation analysis for detecting differential imaging genetics modules"],"prefix":"10.1093","volume":"32","author":[{"given":"Jian","family":"Fang","sequence":"first","affiliation":[{"name":"1Biomedical Engineering Department, Tulane University, New Orleans, LA 70118, USA"},{"name":"2School of Mathematics and Statistics, Xi\u2019an Jiaotong University, Xi\u2019an, ShaanXi 710049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongdong","family":"Lin","sequence":"additional","affiliation":[{"name":"3The Mind Research Network, Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM 87131, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S. Charles","family":"Schulz","sequence":"additional","affiliation":[{"name":"4Department of Psychiatry, University of Minnesota, Minneapolis, MN 55455, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zongben","family":"Xu","sequence":"additional","affiliation":[{"name":"2School of Mathematics and Statistics, Xi\u2019an Jiaotong University, Xi\u2019an, ShaanXi 710049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vince D.","family":"Calhoun","sequence":"additional","affiliation":[{"name":"3The Mind Research Network, Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM 87131, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Ping","family":"Wang","sequence":"additional","affiliation":[{"name":"1Biomedical Engineering Department, Tulane University, New Orleans, LA 70118, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,7,27]]},"reference":[{"key":"2023020113524855500_btw485-B1","author":"Andrew","year":"2013"},{"key":"2023020113524855500_btw485-B2","author":"Baron","year":"2005"},{"key":"2023020113524855500_btw485-B3","doi-asserted-by":"crossref","first-page":"2137","DOI":"10.1093\/bioinformatics\/btt341","article-title":"Joint analysis of expression profiles from multiple cancers improves the identification of microrna\u2013gene interactions","volume":"29","author":"Chen","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020113524855500_btw485-B4","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1111\/j.1467-9868.2009.00723.x","article-title":"Sparse partial least squares regression for simultaneous dimension reduction and variable selection","volume":"72","author":"Chun","year":"2010","journal-title":"J. R. Stat. Soc. Ser. B (Stat. Methodol.)"},{"key":"2023020113524855500_btw485-B5","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1111\/rssb.12033","article-title":"The joint graphical lasso for inverse covariance estimation across multiple classes","volume":"76","author":"Danaher","year":"2014","journal-title":"J. R. Stat. Soc. Ser. B (Stat. Methodol.)"},{"key":"2023020113524855500_btw485-B6","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1109\/TBME.2013.2292588","article-title":"Common copy number variation detection from multiple sequenced samples","volume":"61","author":"Duan","year":"2014","journal-title":"IEEE Trans. Biomed. Eng"},{"key":"2023020113524855500_btw485-B7","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/sj.mp.4002049","article-title":"CNTNAP2 gene dosage variation is associated with schizophrenia and epilepsy","volume":"13","author":"Friedman","year":"2008","journal-title":"Mol. Psychiatry"},{"key":"2023020113524855500_btw485-B8","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1007\/s12021-013-9184-3","article-title":"The MCIC collection: a shared repository of multi-modal, multi-site brain image data from a clinical investigation of schizophrenia","volume":"11","author":"Gollub","year":"2013","journal-title":"Neuroinformatics"},{"key":"2023020113524855500_btw485-B9","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/j.neuroimage.2014.12.025","article-title":"Comparison of variants of canonical correlation analysis and partial least squares for combined analysis of MRI and genetic data","volume":"107","author":"Grellmann","year":"2015","journal-title":"NeuroImage"},{"key":"2023020113524855500_btw485-B10","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1016\/j.neuroimage.2009.12.109","article-title":"The role of the right inferior frontal gyrus: inhibition and attentional control","volume":"50","author":"Hampshire","year":"2010","journal-title":"NeuroImage"},{"key":"2023020113524855500_btw485-B11","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1016\/j.biopsych.2005.11.005","article-title":"Imaging genetics: perspectives from studies of genetically driven variation in serotonin function and corticolimbic affective processing","volume":"59","author":"Hariri","year":"2006","journal-title":"Biol. Psychiatry"},{"key":"2023020113524855500_btw485-B12","author":"Hocking","year":"2011"},{"key":"2023020113524855500_btw485-B13","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1198\/jcgs.2010.09208","article-title":"A path algorithm for the fused lasso signal approximator","volume":"19","author":"Hoefling","year":"2010","journal-title":"J. Comput. Graph. Stat"},{"key":"2023020113524855500_btw485-B14","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1093\/biomet\/28.3-4.321","article-title":"Relations between two sets of variates","volume":"28","author":"Hotelling","year":"1936","journal-title":"Biometrika"},{"key":"2023020113524855500_btw485-B15","doi-asserted-by":"crossref","first-page":"3242","DOI":"10.1093\/brain\/awt264","article-title":"Midbrain dopamine function in schizophrenia and depression: a post-mortem and positron emission tomographic imaging study","volume":"136","author":"Howes","year":"2013","journal-title":"Brain"},{"key":"2023020113524855500_btw485-B16","doi-asserted-by":"crossref","first-page":"D793","DOI":"10.1093\/nar\/gks1055","article-title":"The consensusPathDB interaction database: 2013 update","volume":"41","author":"Kamburov","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023020113524855500_btw485-B17","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023020113524855500_btw485-B18","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1093\/brain\/awl386","article-title":"Volume, neuron density and total neuron number in five subcortical regions in schizophrenia","volume":"130","author":"Kreczmanski","year":"2007","journal-title":"Brain"},{"key":"2023020113524855500_btw485-B19","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1142\/S012906570000034X","article-title":"Kernel and nonlinear canonical correlation analysis","volume":"10","author":"Lai","year":"2000","journal-title":"Int. J. Neural Syst"},{"key":"2023020113524855500_btw485-B20","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1038\/ejhg.2013.69","article-title":"Kernel canonical correlation analysis for assessing gene\u2013gene interactions and application to ovarian cancer","volume":"22","author":"Larson","year":"2014","journal-title":"Eur. J. Hum. Genet"},{"key":"2023020113524855500_btw485-B21","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/sj.mp.4001819","article-title":"The role of phospholipases A2 in schizophrenia","volume":"11","author":"Law","year":"2006","journal-title":"Mol. Psychiatry"},{"key":"2023020113524855500_btw485-B22","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1002\/ajmg.b.30481","article-title":"Towards understanding the schizophrenia code: an expanded convergent functional genomics approach","volume":"144","author":"Le-Niculescu","year":"2007","journal-title":"Am. J. Med. Genet. B"},{"key":"2023020113524855500_btw485-B23","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1016\/j.media.2013.10.010","article-title":"Correspondence between fMRI and SNP data by group sparse canonical correlation analysis","volume":"18","author":"Lin","year":"2014","journal-title":"Med. Image Anal"},{"key":"2023020113524855500_btw485-B24","doi-asserted-by":"crossref","first-page":"262","DOI":"10.3389\/fninf.2014.00029","article-title":"A review of multivariate analyses in imaging genetics","volume":"8","author":"Liu","year":"2014","journal-title":"Front. Neuroinf"},{"key":"2023020113524855500_btw485-B25","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1109\/LSP.2008.922513","article-title":"A parallel independent component analysis approach to investigate genomic influence on brain function","volume":"15","author":"Liu","year":"2008","journal-title":"IEEE Signal Process. Lett"},{"key":"2023020113524855500_btw485-B26","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/0893-133X(95)00150-C","article-title":"Dopamine receptor mRNA expression in human striatum and neocortex","volume":"15","author":"Meador-Woodruff","year":"1996","journal-title":"Neuropsychopharmacology"},{"key":"2023020113524855500_btw485-B27","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1111\/j.1467-9868.2010.00740.x","article-title":"Stability selection","volume":"72","author":"Meinshausen","year":"2010","journal-title":"J. R. Stat. Soc. Ser. B (Stat. Methodol.)"},{"key":"2023020113524855500_btw485-B28","doi-asserted-by":"crossref","first-page":"1286","DOI":"10.1016\/j.neuroimage.2011.10.063","article-title":"The future of fMRI and genetics research","volume":"62","author":"Meyer-Lindenberg","year":"2012","journal-title":"NeuroImage"},{"key":"2023020113524855500_btw485-B29","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1038\/mp.2010.7","article-title":"Molecular pathways involved in neuronal cell adhesion and membrane scaffolding contribute to schizophrenia and bipolar disorder susceptibility","volume":"16","author":"O\u2019Dushlaine","year":"2011","journal-title":"Mol. Psychiatry"},{"key":"2023020113524855500_btw485-B30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2202\/1544-6115.1406","article-title":"Sparse canonical correlation analysis with application to genomic data integration","volume":"8","author":"Parkhomenko","year":"2009","journal-title":"Stat. Appl. Genet. Mol. Biol"},{"key":"2023020113524855500_btw485-B31","doi-asserted-by":"crossref","first-page":"276","DOI":"10.3389\/fgene.2015.00276","article-title":"An introductory review of parallel independent component analysis (p-ICA) and a guide to applying p-ICA to genetic data and imaging phenotypes to identify disease-associated biological pathways and systems in common complex disorders","volume":"6","author":"Pearlson","year":"2015","journal-title":"Front. Genet"},{"key":"2023020113524855500_btw485-B32","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1016\/S0006-8993(99)01123-3","article-title":"Differential alteration of phospholipase A2 activities in brain of patients with schizophrenia","volume":"821","author":"Ross","year":"1999","journal-title":"Brain Res"},{"key":"2023020113524855500_btw485-B33","doi-asserted-by":"crossref","first-page":"5001","DOI":"10.1093\/hmg\/ddt350","article-title":"Transcriptome study of differential expression in schizophrenia","volume":"22","author":"Sanders","year":"2013","journal-title":"Hum. Mol. Genet"},{"key":"2023020113524855500_btw485-B34","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/s12918-014-0087-1","article-title":"Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks","volume":"8","author":"Tian","year":"2014","journal-title":"BMC Syst. Biol"},{"key":"2023020113524855500_btw485-B35","doi-asserted-by":"crossref","first-page":"E3","DOI":"10.1503\/jpn.150092","article-title":"Aberrant network connectivity during error processing in patients with schizophrenia","volume":"41","author":"Voegler","year":"2016","journal-title":"J. Psychiatry Neurosci. JPN"},{"key":"2023020113524855500_btw485-B36","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1016\/j.neuroimage.2010.07.002","article-title":"Discovering genetic associations with high-dimensional neuroimaging phenotypes: a sparse reduced-rank regression approach","volume":"53","author":"Vounou","year":"2010","journal-title":"NeuroImage"},{"key":"2023020113524855500_btw485-B37","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1016\/j.schres.2010.09.002","article-title":"A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder","volume":"124","author":"Wang","year":"2010","journal-title":"Schizophrenia Res"},{"key":"2023020113524855500_btw485-B38","doi-asserted-by":"crossref","first-page":"2693","DOI":"10.1093\/bioinformatics\/btu361","article-title":"Network-guided regression for detecting associations between DNA methylation and gene expression","volume":"30","author":"Wang","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020113524855500_btw485-B39","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1002\/ajmg.b.31241","article-title":"Genetic variation in CNTNAP2 alters brain function during linguistic processing in healthy individuals","volume":"156","author":"Whalley","year":"2011","journal-title":"Am. J. Med. Genet. B Neuropsychiatric Genet"},{"key":"2023020113524855500_btw485-B40","doi-asserted-by":"crossref","first-page":"1","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"},{"key":"2023020113524855500_btw485-B41","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1093\/biostatistics\/kxp008","article-title":"A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis","volume":"10","author":"Witten","year":"2009","journal-title":"Biostatistics"},{"key":"2023020113524855500_btw485-B42","first-page":"581","article-title":"Partial least squares","volume":"6","author":"Wold","year":"1985","journal-title":"Encyclopedia Stat. Sci"},{"key":"2023020113524855500_btw485-B43","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.schres.2010.08.027","article-title":"The role of the insula in schizophrenia","volume":"123","author":"Wylie","year":"2010","journal-title":"Schizophrenia Res"},{"key":"2023020113524855500_btw485-B44","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1097\/YPG.0b013e32834acc85","article-title":"Association between schizophrenia and single nucleotide polymorphisms in lipoprotein lipase gene in a Han Chinese population","volume":"21","author":"Xie","year":"2011","journal-title":"Psychiatric Genet"},{"key":"2023020113524855500_btw485-B45","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1137\/130936397","article-title":"Fused multiple graphical lasso","volume":"25","author":"Yang","year":"2015","journal-title":"SIAM J. Optim"},{"key":"2023020113524855500_btw485-B46","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1016\/j.biopsych.2011.07.028","article-title":"Reduced proactive inhibition in schizophrenia is related to corticostriatal dysfunction and poor working memory","volume":"70","author":"Zandbelt","year":"2011","journal-title":"Biol. Psychiatry"},{"key":"2023020113524855500_btw485-B47","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1093\/schbul\/sbv221","article-title":"Working memory in unaffected relatives of patients with schizophrenia: A meta-analysis of functional magnetic resonance imaging studies","volume":"42","author":"Zhang","year":"2016","journal-title":"Schizophrenia Bull"},{"key":"2023020113524855500_btw485-B48","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1109\/TNNLS.2012.2197412","article-title":"l1\/2 regularization: a thresholding representation theory and a fast solver","volume":"23","author":"Zongben","year":"2012","journal-title":"IEEE Trans. Neural Netw. Learn. Syst"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/22\/3480\/49026923\/bioinformatics_32_22_3480.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/22\/3480\/49026923\/bioinformatics_32_22_3480.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T23:55:48Z","timestamp":1675295748000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/22\/3480\/2525602"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,7,27]]},"references-count":48,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2016,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw485","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2016,11,15]]},"published":{"date-parts":[[2016,7,27]]}}}