{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T16:16:59Z","timestamp":1764173819320,"version":"3.37.3"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"5","funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: High-throughput technologies can identify genes whose expression profiles correlate with specific phenotypes; however, placing these genes into a biological context remains challenging. To help address this issue, we developed nested Expression Analysis Systematic Explorer (nEASE). nEASE complements traditional gene ontology enrichment approaches by determining statistically enriched gene ontology subterms within a list of genes based on co-annotation. Here, we overview an open-source software version of the nEASE algorithm. nEASE can be used either stand-alone or as part of a pathway discovery pipeline.<\/jats:p>\n               <jats:p>Availability: nEASE is implemented within the Multiple Experiment Viewer software package available at http:\/\/www.tm4.org\/mev.<\/jats:p>\n               <jats:p>Contact: \u00a0cholmes@stats.ox.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts011","type":"journal-article","created":{"date-parts":[[2012,1,14]],"date-time":"2012-01-14T01:50:47Z","timestamp":1326505847000},"page":"726-728","source":"Crossref","is-referenced-by-count":6,"title":["nEASE: a method for gene ontology subclassification of high-throughput gene expression data"],"prefix":"10.1093","volume":"28","author":[{"given":"Thomas W.","family":"Chittenden","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"},{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"},{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"},{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eleanor A.","family":"Howe","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"},{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennifer M.","family":"Taylor","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica C.","family":"Mar","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"},{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"},{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin J.","family":"Aryee","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"},{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harold","family":"G\u00f3mez","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Razvan","family":"Sultana","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Braisted","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarita J.","family":"Nair","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Quackenbush","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"},{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"},{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Holmes","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"},{"name":"1 Department of Biostatistics and Computational Biology, 2Department of Cancer Biology, Dana-Farber Cancer Institute, 3Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 4Department of Statistics, University of Oxford, Oxford, UK, 5Bioinformatics Group, CSIRO Plant Industry, Canberra ACT, Australia, 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 7Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, 8J. Craig Venter Institute, Rockville, MD, USA and 9MRC Mammalian Genetics Unit, Harwell, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,1,13]]},"reference":[{"key":"2023012512202274700_B1","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1186\/1471-2105-8-114","article-title":"From genes to functional classes in the study of biological systems","volume":"8","author":"Al-Shahrour","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023012512202274700_B2","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/bioinformatics\/btl140","article-title":"Improved scoring of functional groups from gene expression data by decorrelating GO graph structure","volume":"22","author":"Alexa","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012512202274700_B3","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2023012512202274700_B4","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1093\/bioinformatics\/btn250","article-title":"Ontologizer 2.0\u2013a multifunctional tool for GO term enrichment analysis and data exploration","volume":"24","author":"Bauer","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012512202274700_B5","doi-asserted-by":"crossref","first-page":"3710","DOI":"10.1093\/bioinformatics\/bth456","article-title":"GO: TermFinder\u2013open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes","volume":"20","author":"Boyle","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012512202274700_B6","doi-asserted-by":"crossref","first-page":"3775","DOI":"10.1093\/nar\/gkg624","article-title":"Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate","volume":"31","author":"Draghici","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012512202274700_B7","first-page":"98","article-title":"Global functional profiling of gene expression","volume":"81","author":"Draghici","year":"2003","journal-title":"Genomics"},{"key":"2023012512202274700_B8","doi-asserted-by":"crossref","first-page":"3024","DOI":"10.1093\/bioinformatics\/btm440","article-title":"Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis","volume":"23","author":"Grossmann","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012512202274700_B9","doi-asserted-by":"crossref","first-page":"R70","DOI":"10.1186\/gb-2003-4-10-r70","article-title":"Identifying biological themes within lists of genes with EASE","volume":"4","author":"Hosack","year":"2003","journal-title":"Genome Biol."},{"key":"2023012512202274700_B10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"Huang","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012512202274700_B11","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1093\/bioinformatics\/btl599","article-title":"Extensions to gene set enrichment","volume":"23","author":"Jiang","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012512202274700_B12","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1006\/geno.2002.6698","article-title":"Profiling gene expression using onto-express","volume":"79","author":"Khatri","year":"2002","journal-title":"Genomics"},{"key":"2023012512202274700_B13","doi-asserted-by":"crossref","first-page":"W449","DOI":"10.1093\/nar\/gkh409","article-title":"Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments","volume":"32","author":"Khatri","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012512202274700_B14","doi-asserted-by":"crossref","first-page":"13550","DOI":"10.1073\/pnas.0506230102","article-title":"An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival","volume":"102","author":"Miller","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012512202274700_B15","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/S0076-6879(06)11009-5","article-title":"TM4 microarray software suite","volume":"411","author":"Saeed","year":"2006","journal-title":"Methods Enzymol."},{"key":"2023012512202274700_B16","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012512202274700_B17","doi-asserted-by":"crossref","first-page":"R28","DOI":"10.1186\/gb-2003-4-4-r28","article-title":"GoMiner: a resource for biological interpretation of genomic and proteomic data","volume":"4","author":"Zeeberg","year":"2003","journal-title":"Genome Biol."},{"key":"2023012512202274700_B18","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1093\/bioinformatics\/btq059","article-title":"GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach","volume":"26","author":"Zhang","year":"2010","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/5\/726\/48879493\/bioinformatics_28_5_726.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/5\/726\/48879493\/bioinformatics_28_5_726.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:38:17Z","timestamp":1674661097000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/5\/726\/247925"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1,13]]},"references-count":18,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2012,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts011","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"type":"electronic","value":"1367-4811"},{"type":"print","value":"1367-4803"}],"subject":[],"published-other":{"date-parts":[[2012,3,1]]},"published":{"date-parts":[[2012,1,13]]}}}