{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T09:22:11Z","timestamp":1775640131155,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We previously developed dmGWAS to search for dense modules in a human protein\u2013protein interaction (PPI) network; it has since become a popular tool for network-assisted analysis of genome-wide association studies (GWAS). dmGWAS weights nodes by using GWAS signals. Here, we introduce an upgraded algorithm, EW_dmGWAS, to boost GWAS signals in a node- and edge-weighted PPI network. In EW_dmGWAS, we utilize condition-specific gene expression profiles for edge weights. Specifically, differential gene co-expression is used to infer the edge weights. We applied EW_dmGWAS to two diseases and compared it with other relevant methods. The results suggest that EW_dmGWAS is more powerful in detecting disease-associated signals.<\/jats:p>\n               <jats:p>Availability and implementation: The algorithm of EW_dmGWAS is implemented in the R package dmGWAS_3.0 and is available at http:\/\/bioinfo.mc.vanderbilt.edu\/dmGWAS.<\/jats:p>\n               <jats:p>Contact: \u00a0zhongming.zhao@vanderbilt.edu or peilin.jia@vanderbilt.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary materials are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv150","type":"journal-article","created":{"date-parts":[[2015,3,25]],"date-time":"2015-03-25T03:18:04Z","timestamp":1427253484000},"page":"2591-2594","source":"Crossref","is-referenced-by-count":56,"title":["EW_dmGWAS: edge-weighted dense module search for genome-wide association studies and gene expression profiles"],"prefix":"10.1093","volume":"31","author":[{"given":"Quan","family":"Wang","sequence":"first","affiliation":[{"name":"1 Department of Biomedical Informatics,"}]},{"given":"Hui","family":"Yu","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics,"}]},{"given":"Zhongming","family":"Zhao","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics,"},{"name":"2 Center for Quantitative Sciences,"},{"name":"3 Department of Psychiatry and"},{"name":"4 Department of Cancer Biology, Vanderbilt University, Nashville, TN 37232, USA"}]},{"given":"Peilin","family":"Jia","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics,"},{"name":"2 Center for Quantitative Sciences,"}]}],"member":"286","published-online":{"date-parts":[[2015,3,24]]},"reference":[{"key":"2023051308485825300_btv150-B1","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.schres.2011.11.002","article-title":"SNP-based analysis of neuroactive ligand-receptor interaction pathways implicates PGE2 as a novel mediator of antipsychotic treatment response: data from the CATIE study","volume":"135","author":"Adkins","year":"2012","journal-title":"Schizophr. Res."},{"key":"2023051308485825300_btv150-B2","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1002\/gepi.20448","article-title":"Comparisons of multi-marker association methods to detect association between a candidate region and disease","volume":"34","author":"Ballard","year":"2010","journal-title":"Genet. Epidemiol."},{"key":"2023051308485825300_btv150-B3","doi-asserted-by":"crossref","first-page":"2780","DOI":"10.1093\/hmg\/ddt668","article-title":"Guilt by rewiring: gene prioritization through network rewiring in genome wide association studies","volume":"23","author":"Hou","year":"2014","journal-title":"Hum. Mol. Genet."},{"key":"2023051308485825300_btv150-B4","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1038\/ng2075","article-title":"A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer","volume":"39","author":"Hunter","year":"2007","journal-title":"Nat. Genet."},{"key":"2023051308485825300_btv150-B5","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/mp.2009.93","article-title":"SZGR: a comprehensive schizophrenia gene resource","volume":"15","author":"Jia","year":"2010","journal-title":"Mol. Psychiatry."},{"key":"2023051308485825300_btv150-B6","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1093\/bioinformatics\/btq615","article-title":"dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks","volume":"27","author":"Jia","year":"2011","journal-title":"Bioinformatics"},{"key":"2023051308485825300_btv150-B7","doi-asserted-by":"crossref","first-page":"e1002587","DOI":"10.1371\/journal.pcbi.1002587","article-title":"Network-assisted investigation of combined causal signals from genome-wide association studies in schizophrenia","volume":"8","author":"Jia","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"2023051308485825300_btv150-B8","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.ajhg.2010.06.009","article-title":"A versatile gene-based test for genome-wide association studies","volume":"87","author":"Liu","year":"2010","journal-title":"Am. J. Hum. Genet."},{"key":"2023051308485825300_btv150-B9","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1093\/bioinformatics\/btr136","article-title":"COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method","volume":"27","author":"Ma","year":"2011","journal-title":"Bioinformatics"},{"key":"2023051308485825300_btv150-B10","doi-asserted-by":"crossref","first-page":"W104","DOI":"10.1093\/nar\/gkt387","article-title":"MetaRanker 2.0: a web server for prioritization of genetic variation data","volume":"41","author":"Pers","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023051308485825300_btv150-B11","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nmeth.1282","article-title":"Integrated network analysis platform for protein\u2013protein interactions","volume":"6","author":"Wu","year":"2009","journal-title":"Nat. Methods"},{"issue":"Suppl 5","key":"2023051308485825300_btv150-B12","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1752-0509-7-S5-S2","article-title":"Dynamic protein interaction modules in human hepatocellular carcinoma progression","volume":"7","author":"Yu","year":"2013","journal-title":"BMC Syst. Biol."},{"key":"2023051308485825300_btv150-B13","doi-asserted-by":"crossref","first-page":"W741","DOI":"10.1093\/nar\/gki475","article-title":"WebGestalt: an integrated system for exploring gene sets in various biological contexts","volume":"33","author":"Zhang","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023051308485825300_btv150-B14","article-title":"Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder","author":"Zhao","year":"2014","journal-title":"Mol Psychiatry"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/15\/2591\/50306712\/bioinformatics_31_15_2591.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/15\/2591\/50306712\/bioinformatics_31_15_2591.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T08:49:10Z","timestamp":1683967750000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/15\/2591\/187753"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,3,24]]},"references-count":14,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2015,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv150","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,8,1]]},"published":{"date-parts":[[2015,3,24]]}}}