{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T15:41:27Z","timestamp":1787240487736,"version":"build-2736575974"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: CePa is an R package aiming to find significant pathways through network topology information. The package has several advantages compared with current pathway enrichment tools. First, pathway node instead of single gene is taken as the basic unit when analysing networks to meet the fact that genes must be constructed into complexes to hold normal functions. Second, multiple network centralities are applied simultaneously to measure importance of nodes from different aspects to make a full view on the biological system. CePa extends standard pathway enrichment methods, which include both over-representation analysis procedure and gene-set analysis procedure. CePa has been evaluated with high performance on real-world data, and it can provide more information directly related to current biological problems.<\/jats:p>\n                  <jats:p>Availability: CePa is available at the Comprehensive R Archive Network (CRAN): http:\/\/cran.r-project.org\/web\/packages\/CePa\/<\/jats:p>\n                  <jats:p>Contact: \u00a0jwang@nju.edu.cn<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt008","type":"journal-article","created":{"date-parts":[[2013,1,11]],"date-time":"2013-01-11T20:24:22Z","timestamp":1357935862000},"page":"658-660","source":"Crossref","is-referenced-by-count":61,"title":["CePa: an R package for finding significant pathways weighted by multiple network centralities"],"prefix":"10.1093","volume":"29","author":[{"given":"Zuguang","family":"Gu","sequence":"first","affiliation":[{"name":"1 The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science and 2Key Laboratory of Advanced Photonic and Electronic Materials, Department of Physics, Nanjing University, Nanjing 210093, China"},{"name":"1 The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science and 2Key Laboratory of Advanced Photonic and Electronic Materials, Department of Physics, Nanjing University, Nanjing 210093, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin","family":"Wang","sequence":"additional","affiliation":[{"name":"1 The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science and 2Key Laboratory of Advanced Photonic and Electronic Materials, Department of Physics, Nanjing University, Nanjing 210093, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,1,10]]},"reference":[{"key":"2023051607330832700_btt008-B1","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/1471-2105-10-47","article-title":"A general modular framework for gene set enrichment analysis","volume":"10","author":"Ackermann","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023051607330832700_btt008-B2","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1186\/1471-2105-8-242","article-title":"Improving gene set analysis of microarray data by SAM-GS","volume":"8","author":"Dinu","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023051607330832700_btt008-B3","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1101\/gr.6202607","article-title":"A systems biology approach for pathway level analysis","volume":"17","author":"Draghici","year":"2007","journal-title":"Genome Res."},{"key":"2023051607330832700_btt008-B4","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1214\/07-AOAS101","article-title":"On testing the significance of sets of genes","volume":"1","author":"Efron","year":"2007","journal-title":"Ann. Appl. Stat."},{"key":"2023051607330832700_btt008-B5","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1093\/bioinformatics\/btq131","article-title":"TopoGSA: network topological gene set analysis","volume":"26","author":"Glaab","year":"2010","journal-title":"Bioinformatics"},{"key":"2023051607330832700_btt008-B6","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1186\/1752-0509-6-56","article-title":"Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes","volume":"6","author":"Gu","year":"2012","journal-title":"BMC Syst. Biol."},{"key":"2023051607330832700_btt008-B7","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat. Protoc."},{"key":"2023051607330832700_btt008-B8","doi-asserted-by":"crossref","first-page":"3587","DOI":"10.1093\/bioinformatics\/bti565","article-title":"Ontological analysis of gene expression data: current tools, limitations, and open problems","volume":"21","author":"Khatri","year":"2005","journal-title":"Bioinformatics"},{"key":"2023051607330832700_btt008-B9","doi-asserted-by":"crossref","first-page":"2347","DOI":"10.1093\/bioinformatics\/btq430","article-title":"Cytoscape Web: an interactive web-based network browser","volume":"26","author":"Lopes","year":"2010","journal-title":"Bioinformatics"},{"key":"2023051607330832700_btt008-B10","doi-asserted-by":"crossref","first-page":"D674","DOI":"10.1093\/nar\/gkn653","article-title":"PID: the pathway interaction database","volume":"37","author":"Schaefer","year":"2009","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/5\/658\/50335798\/bioinformatics_29_5_658.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/5\/658\/50335798\/bioinformatics_29_5_658.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T03:56:13Z","timestamp":1684209373000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/5\/658\/251837"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,10]]},"references-count":10,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2013,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt008","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,3,1]]},"published":{"date-parts":[[2013,1,10]]}}}