{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T22:41:10Z","timestamp":1767825670746,"version":"3.49.0"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 2D Difference In-Gel Electrophoresis (2D-DIGE) or 2D gel technology is being used as a routine proteomics technique for biomarker discovery. Analyzing such high-dimensional data requires multivariate analysis techniques to be applied. In addition, protein post-translational modification (PTM) information from the 2D gel data is usually overlooked. We report on an R package, digeR, with an easy to use graphical user interface for analyzing 2D-DIGE (2D gel) data. It provides a tool for visually looking for potential PTM changes from different biological states and support biomarker discovery through multivariate analysis techniques.<\/jats:p>\n               <jats:p>Availability: digeR package is freely available from the CRAN: http:\/\/cran.r-project.org\/web\/packages\/digeR\/index.html.<\/jats:p>\n               <jats:p>Contact: \u00a0yue.fan@ucd.ie<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp514","type":"journal-article","created":{"date-parts":[[2009,8,26]],"date-time":"2009-08-26T03:34:49Z","timestamp":1251257689000},"page":"3033-3034","source":"Crossref","is-referenced-by-count":11,"title":["digeR: a graphical user interface R package for analyzing 2D-DIGE data"],"prefix":"10.1093","volume":"25","author":[{"given":"Yue","family":"Fan","sequence":"first","affiliation":[{"name":"1 UCD School of Medicine and Medical Science, 2UCD Conway Institute of Biomolecular and Biomolecular Research and 3UCD School of Mathematical Sciences, University College Dublin, Dublin 4, Dublin, Ireland"},{"name":"1 UCD School of Medicine and Medical Science, 2UCD Conway Institute of Biomolecular and Biomolecular Research and 3UCD School of Mathematical Sciences, University College Dublin, Dublin 4, Dublin, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"T. Brendan","family":"Murphy","sequence":"additional","affiliation":[{"name":"1 UCD School of Medicine and Medical Science, 2UCD Conway Institute of Biomolecular and Biomolecular Research and 3UCD School of Mathematical Sciences, University College Dublin, Dublin 4, Dublin, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"R. William G.","family":"Watson","sequence":"additional","affiliation":[{"name":"1 UCD School of Medicine and Medical Science, 2UCD Conway Institute of Biomolecular and Biomolecular Research and 3UCD School of Mathematical Sciences, University College Dublin, Dublin 4, Dublin, Ireland"},{"name":"1 UCD School of Medicine and Medical Science, 2UCD Conway Institute of Biomolecular and Biomolecular Research and 3UCD School of Mathematical Sciences, University College Dublin, Dublin 4, Dublin, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,8,25]]},"reference":[{"key":"2023013112151777400_B1","doi-asserted-by":"crossref","first-page":"942","DOI":"10.1021\/pr800570s","article-title":"2D-DIGE as a strategy to identify serum markers for the progression of prostate cancer","volume":"8","author":"Byrne","year":"2009","journal-title":"J. Proteome Res."},{"key":"2023013112151777400_B2","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1093\/bioinformatics\/18.9.1184","article-title":"Determination of minimum sample size and discriminatory expression patterns in microarray data","volume":"18","author":"Hwang","year":"2002","journal-title":"Bioinformatics"},{"key":"2023013112151777400_B3","doi-asserted-by":"crossref","first-page":"5578","DOI":"10.1200\/JCO.2007.13.5392","article-title":"Panel of serum biomarkers for the diagnosis of lung cancer","volume":"25","author":"Patz","year":"2007","journal-title":"J. Clin. Oncol."},{"key":"2023013112151777400_B4","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1038\/nbt1235","article-title":"Protein biomarker discovery and validation: the long and uncertain path to clinical utility","volume":"24","author":"Rifai","year":"2006","journal-title":"Nat Biotechnol."},{"key":"2023013112151777400_B5","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1002\/ijc.23490","article-title":"Haptoglobin-beta chain defined by monoclonal antibody RM2 as a novel serum marker for prostate cancer","volume":"123","author":"Seiichi Saito","year":"2008","journal-title":"Int. J. Cancer"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/22\/3033\/48997136\/bioinformatics_25_22_3033.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/22\/3033\/48997136\/bioinformatics_25_22_3033.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:43:27Z","timestamp":1675190607000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/22\/3033\/179787"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,8,25]]},"references-count":5,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2009,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp514","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,11,15]]},"published":{"date-parts":[[2009,8,25]]}}}