{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T15:16:16Z","timestamp":1774624576876,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Non-negative matrix factorization (NMF) is an increasingly used algorithm for the analysis of complex high-dimensional data. BRB-ArrayTools is a widely used software system for the analysis of gene expression data with almost 9000 registered users in over 65 countries. We have developed a NMF analysis plug-in in BRB-ArrayTools for unsupervised sample clustering of microarray gene expression data. Our analysis tool also incorporates an algorithm for Semi-NMF which can handle both positive and negative elements for log-ratio data. Output includes a heat map of sample clusters and differentially expressed genes with extensive biological annotation. For comparison, output also includes the results of K-means clustering.<\/jats:p>\n               <jats:p>Availability: The NMF analysis plug-in is freely available in BRB-ArrayTools for non-commercial users. BRB-ArrayTools can be downloaded at http:\/\/linus.nci.nih.gov\/BRB-ArrayTools.html. The algorithms used for NMF and Semi-NMF are available at ftp:\/\/linus.nci.nih.gov\/pub\/NMF.<\/jats:p>\n               <jats:p>Contact: rsimon@mail.nih.gov<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp009","type":"journal-article","created":{"date-parts":[[2009,1,9]],"date-time":"2009-01-09T01:25:05Z","timestamp":1231464305000},"page":"545-547","source":"Crossref","is-referenced-by-count":34,"title":["Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools"],"prefix":"10.1093","volume":"25","author":[{"given":"Qihao","family":"Qi","sequence":"first","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, 2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434 and 3The EMMES Corporation, Rockville, MD 20850, USA"}]},{"given":"Yingdong","family":"Zhao","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, 2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434 and 3The EMMES Corporation, Rockville, MD 20850, USA"}]},{"given":"MingChung","family":"Li","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, 2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434 and 3The EMMES Corporation, Rockville, MD 20850, USA"}]},{"given":"Richard","family":"Simon","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, 2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434 and 3The EMMES Corporation, Rockville, MD 20850, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,1,8]]},"reference":[{"key":"2023013110100309600_B1","doi-asserted-by":"crossref","first-page":"4164","DOI":"10.1073\/pnas.0308531101","article-title":"Metagenes and molecular pattern discovery using matrix factorization","volume":"101","author":"Brunet","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013110100309600_B2","doi-asserted-by":"crossref","first-page":"e1000029","DOI":"10.1371\/journal.pcbi.1000029","article-title":"Nonnegative matrix factorization: an analytical and interpretive tool in computational biology","volume":"4","author":"Devarajan","year":"2008","journal-title":"PLoS Comput. Biol."},{"key":"2023013110100309600_B3","doi-asserted-by":"crossref","first-page":"research0036","DOI":"10.1186\/gb-2002-3-7-research0036","article-title":"A prediction-based resampling method for estimating the number of clusters in a dataset","volume":"3","author":"Dudoit","year":"2002","journal-title":"Genome Biol."},{"key":"2023013110100309600_B4","doi-asserted-by":"crossref","DOI":"10.1201\/9780367805302","volume-title":"Classification.","author":"Gordon","year":"1999","edition":"2nd edn"},{"key":"2023013110100309600_B5","doi-asserted-by":"crossref","first-page":"8961","DOI":"10.1073\/pnas.161273698","article-title":"Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments","volume":"98","author":"Kerr","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013110100309600_B6","doi-asserted-by":"crossref","first-page":"1706","DOI":"10.1101\/gr.903503","article-title":"Subsystem identification through dimensionality reduction of large-scale gene expression data","volume":"13","author":"Kim","year":"2003","journal-title":"Genome Res."},{"key":"2023013110100309600_B7","doi-asserted-by":"crossref","first-page":"788","DOI":"10.1038\/44565","article-title":"Learning the parts of objects by nonnegative matrix factorization","volume":"401","author":"Lee","year":"1999","journal-title":"Nature"},{"key":"2023013110100309600_B8","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1109\/ICDM.2006.160","article-title":"The relationships among various nonnegative matrix factorization methods for clustering","volume-title":"Proceedings of the Sixth International Conference on Data Mining.","author":"Li","year":"2006"},{"key":"2023013110100309600_B9","doi-asserted-by":"crossref","first-page":"1462","DOI":"10.1093\/bioinformatics\/18.11.1462","article-title":"Methods of assessing reproducibility of clustering patterns observed in analyses of microarray data","volume":"18","author":"McShane","year":"2002","journal-title":"Bioinformatics"},{"key":"2023013110100309600_B10","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/BF02294245","article-title":"An examination of procedures for determining number of clusters in a data set","volume":"50","author":"Milligan","year":"1985","journal-title":"Psychometrika"},{"key":"2023013110100309600_B11","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1186\/1471-2105-7-366","article-title":"BioNMF: a versatile tool for non-negative matrix factorization in biology","volume":"7","author":"Pascual-Montano","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013110100309600_B12","first-page":"1","article-title":"Analysis of gene expression data using BRB-Array Tools","volume":"2","author":"Simon","year":"2006","journal-title":"Cancer Inform."},{"key":"2023013110100309600_B13","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1111\/1467-9868.00293","article-title":"Estimating the number of clusters in a data set via the gap statistic","volume":"63","author":"Tibshirani","year":"2001","journal-title":"J. R. Stat. Soc. Ser. B Stat. Soc."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/4\/545\/48983771\/bioinformatics_25_4_545.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/4\/545\/48983771\/bioinformatics_25_4_545.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T19:42:11Z","timestamp":1675194131000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/4\/545\/250942"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,1,8]]},"references-count":13,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2009,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp009","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,2,15]]},"published":{"date-parts":[[2009,1,8]]}}}