{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T11:11:37Z","timestamp":1775646697110,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1102,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"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":[[2013,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Gene expression or metabolomics data generated from clinical settings are often associated with multiple metadata (i.e. diagnosis, genotype, gender, etc.). It is of great interest to analyze and to visualize the data in these contexts. Here, we introduce INVEX\u2014a novel web-based tool that integrates the server-side capabilities for data analysis with the browse-based technology for data visualization. INVEX has two key features: (i) flexible differential expression analysis for a wide variety of experimental designs; and (ii) interactive visualization within the context of metadata and biological annotations. INVEX has built-in support for gene\/metabolite annotation and a fully functional heatmap builder.<\/jats:p>\n               <jats:p>Availability and implementation: Freely available at http:\/\/www.invex.ca.<\/jats:p>\n               <jats:p>Contact: \u00a0bob@hancocklab.ubc.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt562","type":"journal-article","created":{"date-parts":[[2013,9,28]],"date-time":"2013-09-28T03:43:59Z","timestamp":1380339839000},"page":"3232-3234","source":"Crossref","is-referenced-by-count":54,"title":["INVEX\u2014a web-based tool for integrative visualization of expression data"],"prefix":"10.1093","volume":"29","author":[{"given":"Jianguo","family":"Xia","sequence":"first","affiliation":[{"name":"1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada V6T 1Z4 and 3Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK"},{"name":"1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada V6T 1Z4 and 3Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ngan H.","family":"Lyle","sequence":"additional","affiliation":[{"name":"1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada V6T 1Z4 and 3Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK"},{"name":"1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada V6T 1Z4 and 3Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew L.","family":"Mayer","sequence":"additional","affiliation":[{"name":"1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada V6T 1Z4 and 3Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK"},{"name":"1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada V6T 1Z4 and 3Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olga M.","family":"Pena","sequence":"additional","affiliation":[{"name":"1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada V6T 1Z4 and 3Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK"},{"name":"1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada V6T 1Z4 and 3Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert E. W.","family":"Hancock","sequence":"additional","affiliation":[{"name":"1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada V6T 1Z4 and 3Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK"},{"name":"1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada V6T 1Z4 and 3Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK"},{"name":"1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada V6T 1Z4 and 3Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,9,26]]},"reference":[{"key":"2023012810484577300_btt562-B1","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"key":"2023012810484577300_btt562-B2","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1093\/bioinformatics\/bts677","article-title":"Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web","volume":"29","author":"Miller","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012810484577300_btt562-B3","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1093\/bioinformatics\/19.2.295","article-title":"Matrix2png: a utility for visualizing matrix data","volume":"19","author":"Pavlidis","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012810484577300_btt562-B4","doi-asserted-by":"crossref","first-page":"7243","DOI":"10.4049\/jimmunol.1001952","article-title":"Endotoxin tolerance represents a distinctive state of alternative polarization (M2) in human mononuclear cells","volume":"186","author":"Pena","year":"2011","journal-title":"J. Immunol."},{"key":"2023012810484577300_btt562-B5","doi-asserted-by":"crossref","first-page":"e19541","DOI":"10.1371\/journal.pone.0019541","article-title":"Gitools: analysis and visualisation of genomic data using interactive heat-maps","volume":"6","author":"Perez-Llamas","year":"2011","journal-title":"PLoS One"},{"key":"2023012810484577300_btt562-B6","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/ng0506-500","article-title":"GenePattern 2.0","volume":"38","author":"Reich","year":"2006","journal-title":"Nat. Genet."},{"key":"2023012810484577300_btt562-B7","doi-asserted-by":"crossref","first-page":"374","DOI":"10.2144\/03342mt01","article-title":"TM4: a free, open-source system for microarray data management and analysis","volume":"34","author":"Saeed","year":"2003","journal-title":"Biotechniques"},{"key":"2023012810484577300_btt562-B8","doi-asserted-by":"crossref","first-page":"3246","DOI":"10.1093\/bioinformatics\/bth349","article-title":"Java Treeview\u2013extensible visualization of microarray data","volume":"20","author":"Saldanha","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012810484577300_btt562-B9","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1007\/0-387-29362-0_23","article-title":"Limma: linear models for microarray data","volume-title":"Bioinformatics and Computational Biology Solutions Using R and Bioconductor","author":"Smyth","year":"2005"},{"key":"2023012810484577300_btt562-B10","doi-asserted-by":"crossref","first-page":"1872","DOI":"10.1093\/bioinformatics\/btt319","article-title":"Network2Canvas: network visualization on a canvas with enrichment analysis","volume":"29","author":"Tan","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012810484577300_btt562-B11","doi-asserted-by":"crossref","first-page":"W63","DOI":"10.1093\/nar\/gkt338","article-title":"INMEX\u2013a web-based tool for integrative meta-analysis of expression data","volume":"41","author":"Xia","year":"2013","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/24\/3232\/48894987\/bioinformatics_29_24_3232.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/24\/3232\/48894987\/bioinformatics_29_24_3232.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:49:23Z","timestamp":1674910163000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/24\/3232\/197589"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,9,26]]},"references-count":11,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2013,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt562","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,12,15]]},"published":{"date-parts":[[2013,9,26]]}}}