{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T13:37:38Z","timestamp":1769607458732,"version":"3.49.0"},"reference-count":21,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2011,2,10]],"date-time":"2011-02-10T00:00:00Z","timestamp":1297296000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1186\/1471-2105-12-52","type":"journal-article","created":{"date-parts":[[2011,2,10]],"date-time":"2011-02-10T08:11:11Z","timestamp":1297325471000},"source":"Crossref","is-referenced-by-count":18,"title":["RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis"],"prefix":"10.1186","volume":"12","author":[{"given":"Barry R","family":"Zeeberg","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongfang","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ari B","family":"Kahn","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Ehler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vinodh N","family":"Rajapakse","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert F","family":"Bonner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacob D","family":"Brown","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian P","family":"Brooks","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vladimir L","family":"Larionov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William","family":"Reinhold","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John N","family":"Weinstein","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yves G","family":"Pommier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,2,10]]},"reference":[{"issue":"4","key":"4425_CR1","doi-asserted-by":"publisher","first-page":"R28","DOI":"10.1186\/gb-2003-4-4-r28","volume":"4","author":"BR Zeeberg","year":"2003","unstructured":"Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, et al.: GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 2003, 4(4):R28. 10.1186\/gb-2003-4-4-r28","journal-title":"Genome Biol"},{"key":"4425_CR2","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1186\/1471-2105-6-168","volume":"6","author":"BR Zeeberg","year":"2005","unstructured":"Zeeberg BR, Qin H, Narasimhan S, Sunshine M, Cao H, Kane DW, Reimers M, Stephens RM, Bryant D, Burt SK, et al.: High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics 2005, 6: 168. 10.1186\/1471-2105-6-168","journal-title":"BMC Bioinformatics"},{"key":"4425_CR3","doi-asserted-by":"crossref","unstructured":"The Gene Ontology (GO) project in 2006 Nucleic Acids Res 2006, (34 Database):D322\u2013326.","DOI":"10.1093\/nar\/gkj021"},{"issue":"1","key":"4425_CR4","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25\u201329. 10.1038\/75556","journal-title":"Nat Genet"},{"key":"4425_CR5","unstructured":"GO slims[ http:\/\/www.geneontology.org\/GO.slims.shtml ]"},{"key":"4425_CR6","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1186\/1471-2105-6-162","volume":"6","author":"P Pehkonen","year":"2005","unstructured":"Pehkonen P, Wong G, T\u00f6r\u00f6nen P: Theme discovery from gene lists for identification and viewing of multiple functional groups. BMC Bioinformatics 2005, 6: 162. 10.1186\/1471-2105-6-162","journal-title":"BMC Bioinformatics"},{"key":"4425_CR7","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/1471-2105-8-41","volume":"8","author":"K Prufer","year":"2007","unstructured":"Prufer K, Muetzel B, Do HD, Weiss G, Khaitovich P, Rahm E, P\u00e4\u00e4bo S, Lachmann M, Enard W: FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 2007, 8: 41. 10.1186\/1471-2105-8-41","journal-title":"BMC Bioinformatics"},{"key":"4425_CR8","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1186\/1471-2105-10-240","volume":"10","author":"T Xu","year":"2009","unstructured":"Xu T, Gu JL, Zhou Y, Du L: Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology. BMC Bioinformatics 2009, 10: 240. 10.1186\/1471-2105-10-240","journal-title":"BMC Bioinformatics"},{"issue":"23","key":"4425_CR9","doi-asserted-by":"publisher","first-page":"3197","DOI":"10.1093\/bioinformatics\/btp553","volume":"25","author":"C Herrmann","year":"2009","unstructured":"Herrmann C, B\u00e9rard S, Tichit L: SimCT: a generic tool to visualize ontology-based relationships for biological objects. Bioinformatics 2009, 25(23):3197\u20133198. 10.1093\/bioinformatics\/btp553","journal-title":"Bioinformatics"},{"issue":"13","key":"4425_CR10","doi-asserted-by":"publisher","first-page":"1600","DOI":"10.1093\/bioinformatics\/btl140","volume":"22","author":"A Alexa","year":"2006","unstructured":"Alexa A, Rahnenfuhrer J, Lengauer T: Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 2006, 22(13):1600\u20131607. 10.1093\/bioinformatics\/btl140","journal-title":"Bioinformatics"},{"key":"4425_CR11","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1093\/nar\/gkn001","volume":"36","author":"Y Lu","year":"2008","unstructured":"Lu Y, Rosenfeld R, Simon I, Nau GJ, Bar-Joseph Z: A probabilistic generative model for GO enrichment Analysis. Nucleic Acids Research 2008, 36: 17. e109 e109","journal-title":"Nucleic Acids Research"},{"issue":"22","key":"4425_CR12","doi-asserted-by":"publisher","first-page":"3024","DOI":"10.1093\/bioinformatics\/btm440","volume":"23","author":"S Grossmann","year":"2007","unstructured":"Grossmann S, Bauer S, Robinson PN, Vingron M: Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis. Bioinformatics 2007, 23(22):3024\u20133031. 10.1093\/bioinformatics\/btm440","journal-title":"Bioinformatics"},{"issue":"11","key":"4425_CR13","doi-asserted-by":"publisher","first-page":"3523","DOI":"10.1093\/nar\/gkq045","volume":"38","author":"S Bauer","year":"2010","unstructured":"Bauer S, Gagneur J, Robinson PN: GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Research 2010, 38(11):3523\u20133532. 10.1093\/nar\/gkq045","journal-title":"Nucleic Acids Research"},{"key":"4425_CR14","doi-asserted-by":"publisher","first-page":"i79","DOI":"10.1093\/bioinformatics\/btq203","volume":"26","author":"AJ Richards","year":"2010","unstructured":"Richards AJ, Muller B, Shotwell M, Cowart LA, Rohrer B, Lu X: Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph. Bioinformatics 2010, 26: i79-i87. 10.1093\/bioinformatics\/btq203","journal-title":"Bioinformatics"},{"issue":"5298","key":"4425_CR15","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1126\/science.275.5298.343","volume":"275","author":"JN Weinstein","year":"1997","unstructured":"Weinstein JN, Myers TG, O'Connor PM, Friend SH, Fornace AJ, Kohn KW, Fojo T, Bates SE, Rubinstein LV, Anderson NL, et al.: An information-intensive approach to the molecular pharmacology of cancer. Science 1997, 275(5298):343\u2013349. 10.1126\/science.275.5298.343","journal-title":"Science"},{"key":"4425_CR16","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1002\/stem.5530120106","volume":"12","author":"JN Weinstein","year":"1994","unstructured":"Weinstein JN, Myers T, Buolamwini J, Raghavan K, Viswanadhan VN, Licht J, Rubinstein LV, Koutsoukos AD, Kohn , Zaharevitz DKW, Grever MR, Monks A, Scudiero DA, Chabner BA, Anderson NL, Paull KD: Predictive statistics and artificial intelligence in the U.S. National Cancer Institute's drug discovery program for cancer and AIDS. Stem Cells 1994, 12: 13\u201322. 10.1002\/stem.5530120106","journal-title":"Stem Cells"},{"issue":"1","key":"4425_CR17","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1093\/bioinformatics\/18.1.207","volume":"18","author":"A Sturn","year":"2002","unstructured":"Sturn A, Quackenbush J, Trajanoski Z: Genesis: cluster analysis of microarray data. Bioinformatics 2002, 18(1):207\u2013208. 10.1093\/bioinformatics\/18.1.207","journal-title":"Bioinformatics"},{"key":"4425_CR18","unstructured":"Fisher's Exact Test[ http:\/\/www.langsrud.com\/fisher.htm ]"},{"key":"4425_CR19","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1186\/1471-2105-11-290","volume":"11","author":"J Wang","year":"2010","unstructured":"Wang J, Zhou X, Zhu J, Zhou C, Zheng Guo Z: Revealing and avoiding bias in semantic similarity scores for protein pairs. BMC Bioinformatics 2010, 11: 290. 10.1186\/1471-2105-11-290","journal-title":"BMC Bioinformatics"},{"key":"4425_CR20","unstructured":"clique decomposition algorithm[ http:\/\/www.cs.ubc.ca\/~murphyk\/nips07NetworkWorkshop\/abstracts\/barber.pdf ]"},{"key":"4425_CR21","doi-asserted-by":"crossref","unstructured":"Ehler M, Rajapakse V, Zeeberg B, Brooks B, Brown J, Czaja W, Bonner R: Analysis of Temporal-spatial Co-variation within Gene Expression Microarray Data in an Organogenesis Model. Proceedings of the 6th International Symposium, ISBRA: 38\u201349 2010 Bioinformatics Research and Applications","DOI":"10.1007\/978-3-642-13078-6_6"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-52.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-12-52\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-52.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,8]],"date-time":"2019-06-08T09:02:58Z","timestamp":1559984578000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-52"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,2,10]]},"references-count":21,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4425"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-52","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,2,10]]},"article-number":"52"}}