{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T15:18:21Z","timestamp":1759331901381,"version":"3.33.0"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: New biological systems technologies give scientists the ability to measure thousands of bio-molecules including genes, proteins, lipids and metabolites. We use domain knowledge, e.g. the Gene Ontology, to guide analysis of such data. By focusing on domain-aggregated results at, say the molecular function level, increased interpretability is available to biological scientists beyond what is possible if results are presented at the gene level.<\/jats:p><jats:p>Results: We use a \u2018top\u2013down\u2019 approach to perform domain aggregation by first combining gene expressions before testing for differentially expressed patterns. This is in contrast to the more standard \u2018bottom\u2013up\u2019 approach, where genes are first tested individually then aggregated by domain knowledge. The benefits are greater sensitivity for detecting signals. Our method, domain-enhanced analysis (DEA) is assessed and compared to other methods using simulation studies and analysis of two publicly available leukemia data sets.<\/jats:p><jats:p>Availability: Our DEA method uses functions available in R (http:\/\/www.r-project.org\/) and SAS (http:\/\/www.sas.com\/). The two experimental data sets used in our analysis are available in R as Bioconductor packages, \u2018ALL\u2019 and \u2018golubEsets\u2019 (http:\/\/www.bioconductor.org\/).<\/jats:p><jats:p>Contact: \u00a0jliu6@stat.ncsu.edu<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm092","type":"journal-article","created":{"date-parts":[[2007,3,23]],"date-time":"2007-03-23T00:18:49Z","timestamp":1174609129000},"page":"1225-1234","source":"Crossref","is-referenced-by-count":19,"title":["Domain-enhanced analysis of microarray data using GO annotations"],"prefix":"10.1093","volume":"23","author":[{"given":"Jiajun","family":"Liu","sequence":"first","affiliation":[{"name":"1 Department of Statistics, North Carolina State University, Raleigh, NC 27695-8203, USA and 2GlaxoSmithKline Research and Development, Research Triangle Park, NC 27709-3398, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacqueline M.","family":"Hughes-Oliver","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, North Carolina State University, Raleigh, NC 27695-8203, USA and 2GlaxoSmithKline Research and Development, Research Triangle Park, NC 27709-3398, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"Jr","given":"J. Alan","family":"Menius","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, North Carolina State University, Raleigh, NC 27695-8203, USA and 2GlaxoSmithKline Research and Development, Research Triangle Park, NC 27709-3398, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,3,22]]},"reference":[{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1093\/bioinformatics\/btg455","article-title":"Fatigo: a web tool for finding significant association of gene ontology terms with groups of genes","volume":"20","author":"Al-Shahrour","year":"2003","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","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":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"1943","DOI":"10.1093\/bioinformatics\/bti260","article-title":"Significance analysis of functional categories in gene expression studies: a structured permutation approach","volume":"21","author":"Barry","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.csda.2004.02.005","article-title":"Pls generalised linear regression","volume":"48","author":"Bastien","year":"2005","journal-title":"Comput. Stat. Data Anal"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"1464","DOI":"10.1093\/bioinformatics\/bth088","article-title":"Gostat: findstatistically overrepresented gene ontologies within a group of genes","volume":"20","author":"Beissbarth","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc., B"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"2502","DOI":"10.1093\/bioinformatics\/btg363","article-title":"Characterizing gene sets with funcassociate","volume":"19","author":"Berriz","year":"2003","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1093\/bioinformatics\/btg114","article-title":"Genemerge\u2013post-genomic analysis, data mining, and hypothesis testing","volume":"19","author":"Castillo-Davis","year":"2003","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"2771","DOI":"10.1182\/blood-2003-09-3243","article-title":"Gene expression profile of adult t-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival","volume":"103","author":"Chiaretti","year":"2004","journal-title":"Blood"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/ng0502-19","article-title":"Genemapp, a new tool for viewing and analyzing microarray data on biological pathways","volume":"31","author":"Dahlquist","year":"2002","journal-title":"Nat. Genet"},{"key":"2023041104475956000_","article-title":"Microarray analysis of b cell chronic leukemia","author":"Dalla-Favera","year":"2001","journal-title":"Program and Abstracts of the FASEB 2001 Conference on Hematological Malignancies"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1016\/0169-7439(93)85002-X","article-title":"Simpls: an alternative approach to partial least squares regression","volume":"18","author":"de Jong","year":"1993","journal-title":"Chemom. Intell. Lab Syst"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1198\/106186005X47697","article-title":"Classification using generalized partial least squares","volume":"14","author":"Ding","year":"2005","journal-title":"J. Comput. Graph. Stat"},{"key":"2023041104475956000_","first-page":"98","article-title":"Global functional profiling of gene expression","volume":"81","author":"Draghici","year":"2003","journal-title":"Genomics"},{"key":"2023041104475956000_","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":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1198\/016214501753382129","article-title":"Empirical bayes analysis of a microarray experiment","volume":"96","author":"Efron","year":"2001","journal-title":"J. Am. Stat. Assoc"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1093\/bioinformatics\/bti114","article-title":"Classification using partial least squares with penalized logistic regression","volume":"21","author":"Fort","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1093\/bioinformatics\/btg382","article-title":"A global test for groups of genes: testing association with a clinical outcome","volume":"20","author":"Goeman","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1126\/science.286.5439.531","article-title":"Molecular classification of cancer: class discovery and class prediction by gene expression monitoring","volume":"286","author":"Golub","year":"1999","journal-title":"Science"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1002\/cem.1180020306","article-title":"Pls regression methods","volume":"2","author":"Hoskuldson","year":"1988","journal-title":"J. Chemom"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"2072","DOI":"10.1093\/bioinformatics\/btg283","article-title":"Linear regression and two-class classification with gene expression data","volume":"19","author":"Huang","year":"2003","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","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"},{"issue":"144","key":"2023041104475956000_","article-title":"Page: parametric analysis of gene set enrichment","volume":"6","author":"Kim","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1186\/1471-2105-6-269","article-title":"Erminej: tool for functional analysis of gene expression data sets","volume":"6","author":"Lee","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"3406","DOI":"10.1093\/bioinformatics\/bth415","article-title":"Dimension reduction methods for microarrays with application to censored survival data","volume":"20","author":"Li","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","article-title":"Molecular pathogenesis of t-cell acute lymphoblastic leukemia","author":"Look","year":"2001","journal-title":"Program and Abstracts of the FASEB 2001 Conference on Hematological Malignancies"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1016\/S0098-1354(96)00311-0","article-title":"Nonlinear partial least squares","volume":"21","author":"Malthouse","year":"1997","journal-title":"Comput. Chem. Eng"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1093\/bioinformatics\/16.11.953","article-title":"Power sage: comparing statistical tests for sage experiments","volume":"16","author":"Man","year":"2000","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1080\/00401706.1996.10484549","article-title":"Iteratively reweighted partial least squares estimation for generalized linear regression","volume":"38","author":"Marx","year":"1996","journal-title":"Technometrics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/ng1180","article-title":"Pgc-1\u03b1-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes","volume":"34","author":"Mootha","year":"2003","journal-title":"Nat. Genet"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"2249","DOI":"10.1093\/bioinformatics\/btl378","article-title":"Adgo: analysis of differentially expressed gene sets using composite go annotation","volume":"22","author":"Nam","year":"2006","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1093\/bioinformatics\/18.9.1216","article-title":"Multi-class cancer classification via partial least squares with gene expression profiles","volume":"18","author":"Nguyen","year":"2002","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1093\/bioinformatics\/18.1.39","article-title":"Tumor classification by partial least squares using microarray gene expression data","volume":"18","author":"Nguyen","year":"2002","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1016\/j.csda.2003.08.001","article-title":"On partial least squares dimentsion reduction from microarray-based classification: a simulation study","volume":"46","author":"Nguyen","year":"2004","journal-title":"Comput. Stat. Data Anal"},{"key":"2023041104475956000_","article-title":"Conference report","volume":"3","author":"Novak","year":"2001","journal-title":"FASEB 2001 Conference on Hemotological Malignancies, Medscape General Medicine"},{"key":"2023041104475956000_","article-title":"A mixture model approach to detecting differentially expressed genes with microarray data","volume-title":"Research Report 2001-011","author":"Pan","year":"2001"},{"key":"2023041104475956000_","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":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"13544","DOI":"10.1073\/pnas.0506577102","article-title":"Discovering statistically significant pathways in expression profiling studies","volume":"102","author":"Tian","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"5116","DOI":"10.1073\/pnas.091062498","article-title":"Signficance analysis of microarrays applied to the ionizing radiation response","volume":"98","author":"Tusher","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/0169-7439(94)85050-X","article-title":"Comparing the predictive accuracy of models using a simple randomization test","volume":"25","author":"van der Voet","year":"1994","journal-title":"Chemom Intell Lab Syst"},{"key":"2023041104475956000_","first-page":"R28","article-title":"Gominer: a resource for biological interpretation of genomic and proteomic data","volume":"4","author":"Zeeberg","year":"2003","journal-title":"Bioinformatics"},{"key":"2023041104475956000_","doi-asserted-by":"crossref","first-page":"3483","DOI":"10.1093\/nar\/gkg598","article-title":"Chipinfo: software for extracting gene annotation and gene ontology information for microarray analysis","volume":"31","author":"Zhong","year":"2003","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/10\/1225\/49812659\/bioinformatics_23_10_1225.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/10\/1225\/49812659\/bioinformatics_23_10_1225.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,15]],"date-time":"2025-01-15T05:19:16Z","timestamp":1736918356000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/10\/1225\/197345"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,3,22]]},"references-count":43,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2007,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm092","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"type":"electronic","value":"1367-4811"},{"type":"print","value":"1367-4803"}],"subject":[],"published-other":{"date-parts":[[2007,5,15]]},"published":{"date-parts":[[2007,3,22]]}}}