{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T04:14:54Z","timestamp":1728360894577},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2004,10,1]],"date-time":"2004-10-01T00:00:00Z","timestamp":1096588800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"},{"start":{"date-parts":[[2004,10,1]],"date-time":"2004-10-01T00:00:00Z","timestamp":1096588800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p>When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures within the paper, can be browsed. We set out to create a CGI application containing many of the features of some of the existing standalone software for the visualization of clustered microarray data.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>We present GeneXplorer, a web application for interactive microarray data visualization and analysis in a web environment. GeneXplorer allows users to browse a microarray dataset in an intuitive fashion. It provides simple access to microarray data over the Internet and uses only HTML and JavaScript to display graphic and annotation information. It provides radar and zoom views of the data, allows display of the nearest neighbors to a gene expression vector based on their Pearson correlations and provides the ability to search gene annotation fields.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusions<\/jats:title>\n                        <jats:p>The software is released under the permissive MIT Open Source license, and the complete documentation and the entire source code are freely available for download from CPAN <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/search.cpan.org\/dist\/Microarray-GeneXplorer\/\">http:\/\/search.cpan.org\/dist\/Microarray-GeneXplorer\/<\/jats:ext-link>.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-5-141","type":"journal-article","created":{"date-parts":[[2004,10,8]],"date-time":"2004-10-08T06:24:20Z","timestamp":1097216660000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["GeneXplorer: an interactive web application for microarray data visualization and analysis"],"prefix":"10.1186","volume":"5","author":[{"given":"Christian A","family":"Rees","sequence":"first","affiliation":[]},{"given":"Janos","family":"Demeter","sequence":"additional","affiliation":[]},{"given":"John C","family":"Matese","sequence":"additional","affiliation":[]},{"given":"David","family":"Botstein","sequence":"additional","affiliation":[]},{"given":"Gavin","family":"Sherlock","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2004,10,1]]},"reference":[{"key":"257_CR1","unstructured":"EPCLUST - Clustering, visualization, and analysis[http:\/\/ep.ebi.ac.uk\/EP\/EPCLUST\/]"},{"key":"257_CR2","unstructured":"GEPAS[http:\/\/gepas.bioinfo.cnio.es\/]"},{"key":"257_CR3","doi-asserted-by":"publisher","first-page":"3461","DOI":"10.1093\/nar\/gkg591","volume":"31","author":"J Herrero","year":"2003","unstructured":"Herrero J, Al-Shahrour F, Diaz-Uriarte R, Mateos A, Vaquerizas JM, Santoyo J, Dopazo J: GEPAS: A web-based resource for microarray gene expression data analysis.\n                           Nucleic Acids Res 2003, 31: 3461\u20133467. 10.1093\/nar\/gkg591","journal-title":"Nucleic Acids Res"},{"key":"257_CR4","unstructured":"FGDP: Functional Genomics Data Pipeline[http:\/\/bioinformatics.fccc.edu\/software\/OpenSource\/FGDP\/FGDP.shtml]"},{"key":"257_CR5","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1093\/bioinformatics\/btg407","volume":"20","author":"JD Grant","year":"2004","unstructured":"Grant JD, Somers LA, Zhang Y, Manion FJ, Bidaut G, Ochs MF: FGDP: functional genomics data pipeline for automated, multiple microarray data analyses.\n                           Bioinformatics 2004, 20: 282\u2013283. 10.1093\/bioinformatics\/btg407","journal-title":"Bioinformatics"},{"key":"257_CR6","unstructured":"MeV: MultiExperiment Viewer[http:\/\/www.tigr.org\/software\/tm4\/mev.html]"},{"key":"257_CR7","doi-asserted-by":"crossref","first-page":"374","DOI":"10.2144\/03342mt01","volume":"34","author":"AI Saeed","year":"2003","unstructured":"Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J: TM4: a free, open-source system for microarray data management and analysis.\n                           Biotechniques 2003, 34: 374\u2013378.","journal-title":"Biotechniques"},{"key":"257_CR8","unstructured":"Eisen Lab Software[http:\/\/rana.lbl.gov\/EisenSoftware.htm]"},{"key":"257_CR9","doi-asserted-by":"publisher","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","volume":"95","author":"MB Eisen","year":"1998","unstructured":"Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns.\n                           Proc Natl Acad Sci U S A 1998, 95: 14863\u201314868. 10.1073\/pnas.95.25.14863","journal-title":"Proc Natl Acad Sci U S A"},{"key":"257_CR10","unstructured":"SourceForge.net: Project Info - Java Treeview[http:\/\/sourceforge.net\/projects\/jtreeview\/]"},{"key":"257_CR11","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1093\/nar\/gkg078","volume":"31","author":"J Gollub","year":"2003","unstructured":"Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, Schroeder M, Brown PO, Botstein D, Sherlock G: The Stanford Microarray Database: data access and quality assessment tools.\n                           Nucleic Acids Res 2003, 31: 94\u201396. 10.1093\/nar\/gkg078","journal-title":"Nucleic Acids Res"},{"key":"257_CR12","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1093\/nar\/29.1.152","volume":"29","author":"G Sherlock","year":"2001","unstructured":"Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM: The Stanford Microarray Database.\n                           Nucleic Acids Res 2001, 29: 152\u2013155. 10.1093\/nar\/29.1.152","journal-title":"Nucleic Acids Res"},{"key":"257_CR13","unstructured":"Stanford MicroArray Database File Format Help[http:\/\/smd.stanford.edu\/help\/formats.shtml]"},{"key":"257_CR14","doi-asserted-by":"publisher","first-page":"1453","DOI":"10.1093\/bioinformatics\/bth078","volume":"20","author":"MJ de Hoon","year":"2004","unstructured":"de Hoon MJ, Imoto S, Nolan J, Miyano S: Open source clustering software.\n                           Bioinformatics 2004, 20: 1453\u20131454. 10.1093\/bioinformatics\/bth078","journal-title":"Bioinformatics"},{"key":"257_CR15","first-page":"26","volume":"1","author":"Glenn E Krasner","year":"1988","unstructured":"Krasner Glenn E, Pope Stephen T: A cookbook for using the model-view controller user interface paradigm in Smalltalk-80.\n                           Journal of Object Oriented Programming 1988, 1: 26\u201349.","journal-title":"Journal of Object Oriented Programming"},{"key":"257_CR16","unstructured":"search.cpan.org: Lincoln D. Stein \/GD[http:\/\/search.cpan.org\/dist\/GD\/]"},{"key":"257_CR17","unstructured":"SMD : List Data for publication[http:\/\/smd.stanford.edu\/cgi-bin\/tools\/display\/listMicroArrayData.pl?tableName=publication]"},{"key":"257_CR18","doi-asserted-by":"publisher","first-page":"RESEARCH0059","DOI":"10.1186\/gb-2002-3-11-research0059","volume":"3","author":"AP Gasch","year":"2002","unstructured":"Gasch AP, Eisen MB: Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering.\n                           Genome Biol 2002, 3: RESEARCH0059. 10.1186\/gb-2002-3-11-research0059","journal-title":"Genome Biol"},{"key":"257_CR19","unstructured":"Prostate Cancer Molecular Subtypes[http:\/\/microarray-pubs.stanford.edu\/cgi-bin\/gx?n=prostate1&rx=5]"},{"key":"257_CR20","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1073\/pnas.0304146101","volume":"101","author":"J Lapointe","year":"2004","unstructured":"Lapointe J, Li C, Higgins JP, van de Rijn M, Bair E, Montgomery K, Ferrari M, Egevad L, Rayford W, Bergerheim U, Ekman P, DeMarzo AM, Tibshirani R, Botstein D, Brown PO, Brooks JD, Pollack JR: Gene expression profiling identifies clinically relevant subtypes of prostate cancer.\n                           Proc Natl Acad Sci U S A 2004, 101: 811\u2013816. 10.1073\/pnas.0304146101","journal-title":"Proc Natl Acad Sci U S A"},{"key":"257_CR21","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1093\/nar\/gkg014","volume":"31","author":"M Diehn","year":"2003","unstructured":"Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA: SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.\n                           Nucleic Acids Res 2003, 31: 219\u2013223. 10.1093\/nar\/gkg014","journal-title":"Nucleic Acids Res"},{"key":"257_CR22","doi-asserted-by":"publisher","first-page":"RESEARCH0046","DOI":"10.1186\/gb-2002-3-9-research0046","volume":"3","author":"PT Spellman","year":"2002","unstructured":"Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert C. J., Jr., Brazma A: Design and implementation of microarray gene expression markup language (MAGE-ML).\n                           Genome Biol 2002, 3: RESEARCH0046. 10.1186\/gb-2002-3-9-research0046","journal-title":"Genome Biol"},{"key":"257_CR23","unstructured":"search.cpan.org: Gavin Sherlock \/Microarray-GeneXplorer[http:\/\/search.cpan.org\/dist\/Microarray-GeneXplorer\/]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-5-141.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-5-141\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-5-141.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:18:21Z","timestamp":1728303501000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-5-141"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,10,1]]},"references-count":23,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2004,12]]}},"alternative-id":["257"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-5-141","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2004,10,1]]},"assertion":[{"value":"21 May 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 October 2004","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 October 2004","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"141"}}