{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T04:09:24Z","timestamp":1759205364107},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Elucidation of human disease similarities has provided new insights into etiology, disease classification and drug repositioning. Since dysfunctional regulation would be manifested as the decoupling of expression correlation, disease similarity (DS) in terms of dysfunctional regulation mechanism (DRM) could be estimated by using a differential coexpression based approach, which is described in a companion paper. Due to the lack of tools for estimating DS from the viewpoint of DRM in public domain, we implemented an R package \u2018DSviaDRM\u2019 to identify significant DS via DRM based on transcriptomic data. DSviaDRM contains five easy-to-use functions, DCEA, DCpathway, DS, comDCGL and comDCGLplot, for identifying disease relationships and showing common differential regulation information shared by similar diseases.<\/jats:p>\n               <jats:p>Availability and implementation: DSviaDRM is available as an R package, with a user\u2019s guide and source code, at http:\/\/cran.r-project.org\/web\/packages\/DSviaDRM\/index.html.<\/jats:p>\n               <jats:p>Contact: \u00a0yyli@scbit.org or yxli@scbit.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv474","type":"journal-article","created":{"date-parts":[[2015,8,15]],"date-time":"2015-08-15T01:29:49Z","timestamp":1439602189000},"page":"3870-3872","source":"Crossref","is-referenced-by-count":5,"title":["DSviaDRM: an R package for estimating disease similarity via dysfunctional regulation mechanism"],"prefix":"10.1093","volume":"31","author":[{"given":"Jing","family":"Yang","sequence":"first","affiliation":[{"name":"1 School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People\u2019s Republic of China,"},{"name":"2 System biology group, Shanghai Center for Bioinformation Technology, Shanghai 201203, People\u2019s Republic of China,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Su-Juan","family":"Wu","sequence":"additional","affiliation":[{"name":"1 School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People\u2019s Republic of China,"},{"name":"2 System biology group, Shanghai Center for Bioinformation Technology, Shanghai 201203, People\u2019s Republic of China,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi-Xue","family":"Li","sequence":"additional","affiliation":[{"name":"1 School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People\u2019s Republic of China,"},{"name":"2 System biology group, Shanghai Center for Bioinformation Technology, Shanghai 201203, People\u2019s Republic of China,"},{"name":"3 Shanghai Industrial Technology Institute, Shanghai 201203, People\u2019s Republic of China and"},{"name":"4 Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai 201203, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuan-Yuan","family":"Li","sequence":"additional","affiliation":[{"name":"2 System biology group, Shanghai Center for Bioinformation Technology, Shanghai 201203, People\u2019s Republic of China,"},{"name":"3 Shanghai Industrial Technology Institute, Shanghai 201203, People\u2019s Republic of China and"},{"name":"4 Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai 201203, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,8,13]]},"reference":[{"key":"2023020202412177700_btv474-B1","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/j.cell.2013.08.030","article-title":"A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk","volume":"155","author":"Blair","year":"2013","journal-title":"Cell"},{"key":"2023020202412177700_btv474-B2","doi-asserted-by":"crossref","first-page":"D1104","DOI":"10.1093\/nar\/gks994","article-title":"The comparative toxicogenomics database: update 2013","volume":"41","author":"Davis","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023020202412177700_btv474-B3","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1016\/j.tig.2010.05.001","article-title":"From \u2018differential expression\u2019 to \u2018differential networking\u2019\u2014identification of dysfunctional regulatory networks in diseases","volume":"26","author":"de la Fuente","year":"2010","journal-title":"Trends Genet."},{"key":"2023020202412177700_btv474-B4","doi-asserted-by":"crossref","first-page":"8685","DOI":"10.1073\/pnas.0701361104","article-title":"The human disease network","volume":"104","author":"Goh","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020202412177700_btv474-B5","doi-asserted-by":"crossref","first-page":"e6536","DOI":"10.1371\/journal.pone.0006536","article-title":"Human disease-drug network based on genomic expression profiles","volume":"4","author":"Hu","year":"2009","journal-title":"PLoS One"},{"key":"2023020202412177700_btv474-B6","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1186\/1471-2105-12-266","article-title":"DOSim: an R package for similarity between diseases based on Disease Ontology","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023020202412177700_btv474-B7","doi-asserted-by":"crossref","first-page":"2637","DOI":"10.1093\/bioinformatics\/btq471","article-title":"DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data","volume":"26","author":"Liu","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020202412177700_btv474-B8","doi-asserted-by":"crossref","first-page":"W137","DOI":"10.1093\/nar\/gku412","article-title":"DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections","volume":"42","author":"Liu","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023020202412177700_btv474-B9","doi-asserted-by":"crossref","first-page":"bat018","DOI":"10.1093\/database\/bat018","article-title":"MalaCards: an integrated compendium for diseases and their annotation","volume":"2013","author":"Rappaport","year":"2013","journal-title":"Database (Oxford)"},{"key":"2023020202412177700_btv474-B10","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1016\/j.ajhg.2008.09.017","article-title":"The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease","volume":"83","author":"Robinson","year":"2008","journal-title":"Am. J. Hum. Genet."},{"key":"2023020202412177700_btv474-B11","doi-asserted-by":"crossref","first-page":"e1000662","DOI":"10.1371\/journal.pcbi.1000662","article-title":"Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets","volume":"6","author":"Suthram","year":"2010","journal-title":"PLoS Comput. Biol."},{"key":"2023020202412177700_btv474-B12","doi-asserted-by":"crossref","first-page":"e79729","DOI":"10.1371\/journal.pone.0079729","article-title":"DCGL v2.0: an R package for unveiling differential regulation from differential co-expression","volume":"8","author":"Yang","year":"2013","journal-title":"PLoS One"},{"key":"2023020202412177700_btv474-B13","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1186\/1471-2105-12-315","article-title":"Link-based quantitative methods to identify differentially coexpressed genes and gene pairs","volume":"12","author":"Yu","year":"2011","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/23\/3870\/49036123\/bioinformatics_31_23_3870.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/23\/3870\/49036123\/bioinformatics_31_23_3870.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:56:17Z","timestamp":1675310177000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/23\/3870\/209516"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,8,13]]},"references-count":13,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2015,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv474","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,12,1]]},"published":{"date-parts":[[2015,8,13]]}}}