{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T06:34:33Z","timestamp":1790836473017,"version":"4.1.0"},"reference-count":59,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1521,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: Eukaryotic gene expression (GE) is subjected to precisely coordinated multi-layer controls, across the levels of epigenetic, transcriptional and post-transcriptional regulations. Recently, the emerging multi-dimensional genomic dataset has provided unprecedented opportunities to study the cross-layer regulatory interplay. In these datasets, the same set of samples is profiled on several layers of genomic activities, e.g. copy number variation (CNV), DNA methylation (DM), GE and microRNA expression (ME). However, suitable analysis methods for such data are currently sparse.<\/jats:p>\n                  <jats:p>Results: In this article, we introduced a sparse Multi-Block Partial Least Squares (sMBPLS) regression method to identify multi-dimensional regulatory modules from this new type of data. A multi-dimensional regulatory module contains sets of regulatory factors from different layers that are likely to jointly contribute to a local \u2018gene expression factory\u2019. We demonstrated the performance of our method on the simulated data as well as on The Cancer Genomic Atlas Ovarian Cancer datasets including the CNV, DM, ME and GE data measured on 230 samples. We showed that majority of identified modules have significant functional and transcriptional enrichment, higher than that observed in modules identified using only a single type of genomic data. Our network analysis of the modules revealed that the CNV, DM and microRNA can have coupled impact on expression of important oncogenes and tumor suppressor genes.<\/jats:p>\n                  <jats:p>Availability and implementation: The source code implemented by MATLAB is freely available at: http:\/\/zhoulab.usc.edu\/sMBPLS\/.<\/jats:p>\n                  <jats:p>Contact: \u00a0xjzhou@usc.edu<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary material are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts476","type":"journal-article","created":{"date-parts":[[2012,8,4]],"date-time":"2012-08-04T00:24:37Z","timestamp":1344039877000},"page":"2458-2466","source":"Crossref","is-referenced-by-count":134,"title":["Identifying multi-layer gene regulatory modules from multi-dimensional genomic data"],"prefix":"10.1093","volume":"28","author":[{"given":"Wenyuan","family":"Li","sequence":"first","affiliation":[{"name":"1 Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA, 2National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China and 3Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan, Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shihua","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA, 2National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China and 3Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan, Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chun-Chi","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA, 2National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China and 3Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan, Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianghong Jasmine","family":"Zhou","sequence":"additional","affiliation":[{"name":"1 Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA, 2National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China and 3Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan, Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,8,3]]},"reference":[{"key":"2023012513065202500_bts476-B1","doi-asserted-by":"crossref","first-page":"10101","DOI":"10.1073\/pnas.97.18.10101","article-title":"Singular value decomposition for genome-wide expression data processing and modeling","volume":"97","author":"Alter","year":"2000","journal-title":"Proc. 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Cancer Res."},{"key":"2023012513065202500_bts476-B34","doi-asserted-by":"crossref","first-page":"18371","DOI":"10.1073\/pnas.0709146104","article-title":"A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies","volume":"104","author":"Omberg","year":"2007","journal-title":"Proc. Natl. Acad. 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Multivar. Anal."},{"key":"2023012513065202500_bts476-B41","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1038\/nrc1951","article-title":"The NCI60 human tumour cell line anticancer drug screen","volume":"6","author":"Shoemaker","year":"2006","journal-title":"Nat. Rev. Cancer"},{"key":"2023012513065202500_bts476-B42","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1242\/dev.129.2.329","article-title":"Pitx2 is required at multiple stages of pituitary organogenesis: pituitary primordium formation and cell specification","volume":"129","author":"Suh","year":"2002","journal-title":"Develop. (Cambridge, England)"},{"key":"2023012513065202500_bts476-B43","doi-asserted-by":"crossref","first-page":"5959","DOI":"10.1073\/pnas.0701068104","article-title":"Metagene projection for cross-platform, cross-species characterization of global transcriptional states","volume":"104","author":"Tamayo","year":"2007","journal-title":"Proc. Natl. Acad. 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B (Methodological)"},{"key":"2023012513065202500_bts476-B48","doi-asserted-by":"crossref","first-page":"R96","DOI":"10.1186\/gb-2010-11-9-r96","article-title":"Multi-species integrative biclustering","volume":"11","author":"Waltman","year":"2010","journal-title":"Genome Biol."},{"key":"2023012513065202500_bts476-B49","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1002\/cem.1180030104","article-title":"A multiblock partial least squares algorithm for investigating complex chemical systems","volume":"3","author":"Wangen","year":"1988","journal-title":"J. Chemometr."},{"key":"2023012513065202500_bts476-B50","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1002\/mc.20413","article-title":"Loss of trimethylation at lysine 27 of histone H3 is a predictor of poor outcome in breast, ovarian, and pancreatic cancers","volume":"47","author":"Wei","year":"2008","journal-title":"Mol. Carcinogen."},{"key":"2023012513065202500_bts476-B51","doi-asserted-by":"crossref","first-page":"2214","DOI":"10.1002\/ijc.24599","article-title":"HOXA methylation in normal endometrium from premenopausal women is associated with the presence of ovarian cancer: a proof of principle study","volume":"125","author":"Widschwendter","year":"2009","journal-title":"Int. J. Cancer"},{"key":"2023012513065202500_bts476-B52","article-title":"Extensions of sparse canonical correlation analysis with applications to genomic data","volume":"8","author":"Witten","year":"2009"},{"key":"2023012513065202500_bts476-B53","article-title":"PLS modeling with latent variable in two or more dimensions","author":"Wold","year":"1987","journal-title":"Proc. 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