{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T05:22:32Z","timestamp":1674883352638},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2017,1,27]],"date-time":"2017-01-27T00:00:00Z","timestamp":1485475200000},"content-version":"vor","delay-in-days":1432,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,6,15]]},"abstract":"<jats:p>Summary: The microarrays performed by scientific teams grow exponentially. These microarray data could be useful for researchers around the world, but unfortunately they are underused. To fully exploit these data, it is necessary (i) to extract these data from a repository of the high-throughput gene expression data like Gene Expression Omnibus (GEO) and (ii) to make the data from different microarrays comparable with tools easy to use for scientists. We have developed these two solutions in our server, implementing a database of microarray marker genes (Marker Genes Data Base). This database contains the marker genes of all GEO microarray datasets and it is updated monthly with the new microarrays from GEO. Thus, researchers can see whether the marker genes of their microarray are marker genes in other microarrays in the database, expanding the analysis of their microarray to the rest of the public microarrays. This solution helps not only to corroborate the conclusions regarding a researcher's microarray but also to identify the phenotype of different subsets of individuals under investigation, to frame the results with microarray experiments from other species, pathologies or tissues, to search for drugs that promote the transition between the studied phenotypes, to detect undesirable side effects of the treatment applied, etc. Thus, the researcher can quickly add relevant information to his\/her studies from all of the previous analyses performed in other studies as long as they have been deposited in public repositories.<\/jats:p>\n               <jats:p>Availability: Marker-gene database tool: http:\/\/ibb.uab.es\/mgdb<\/jats:p>\n               <jats:p>Contact: \u00a0jcedano@unorte.edu.uy<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu109","type":"journal-article","created":{"date-parts":[[2014,2,27]],"date-time":"2014-02-27T01:26:41Z","timestamp":1393464401000},"page":"1780-1781","source":"Crossref","is-referenced-by-count":2,"title":["MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes"],"prefix":"10.1093","volume":"30","author":[{"given":"Mario","family":"Huerta","sequence":"first","affiliation":[{"name":"1 \u00a01Institut de Biotecnologia i Biomedicina, 2Escola T\u00e8cnica Superior de Ingenieria, Universitat Aut\u00f2noma de Barcelona; Bellaterra, Barcelona 08193, Spain and 3Laboratorio de Inmunolog\u00eda, Universidad de la Rep\u00fablica Regional Norte-Salto, Rivera 1350, CP 50000 Salto, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Munyi","sequence":"additional","affiliation":[{"name":"1 \u00a01Institut de Biotecnologia i Biomedicina, 2Escola T\u00e8cnica Superior de Ingenieria, Universitat Aut\u00f2noma de Barcelona; Bellaterra, Barcelona 08193, Spain and 3Laboratorio de Inmunolog\u00eda, Universidad de la Rep\u00fablica Regional Norte-Salto, Rivera 1350, CP 50000 Salto, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Exp\u00f3sito","sequence":"additional","affiliation":[{"name":"1 \u00a01Institut de Biotecnologia i Biomedicina, 2Escola T\u00e8cnica Superior de Ingenieria, Universitat Aut\u00f2noma de Barcelona; Bellaterra, Barcelona 08193, Spain and 3Laboratorio de Inmunolog\u00eda, Universidad de la Rep\u00fablica Regional Norte-Salto, Rivera 1350, CP 50000 Salto, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Enric","family":"Querol","sequence":"additional","affiliation":[{"name":"1 \u00a01Institut de Biotecnologia i Biomedicina, 2Escola T\u00e8cnica Superior de Ingenieria, Universitat Aut\u00f2noma de Barcelona; Bellaterra, Barcelona 08193, Spain and 3Laboratorio de Inmunolog\u00eda, Universidad de la Rep\u00fablica Regional Norte-Salto, Rivera 1350, CP 50000 Salto, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan","family":"Cedano","sequence":"additional","affiliation":[{"name":"1 \u00a01Institut de Biotecnologia i Biomedicina, 2Escola T\u00e8cnica Superior de Ingenieria, Universitat Aut\u00f2noma de Barcelona; Bellaterra, Barcelona 08193, Spain and 3Laboratorio de Inmunolog\u00eda, Universidad de la Rep\u00fablica Regional Norte-Salto, Rivera 1350, CP 50000 Salto, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,2,25]]},"reference":[{"key":"2023012711061984000_btu109-B1","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gkq1184","article-title":"NCBI GEO: archive for functional genomics data sets\u201310 years on","volume":"39","author":"Barrett","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012711061984000_btu109-B2","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1186\/1471-2105-10-138","article-title":"PCOPGene-Net: holistic characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships","volume":"10","author":"Huerta","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012711061984000_btu109-B3","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1126\/science.1132939","article-title":"The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease","volume":"313","author":"Lamb","year":"2006","journal-title":"Science"},{"key":"2023012711061984000_btu109-B4","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/419323a","article-title":"Microarray standards at last","volume":"419","author":"Nature","year":"2002","journal-title":"Nature"},{"key":"2023012711061984000_btu109-B5","doi-asserted-by":"crossref","first-page":"D747","DOI":"10.1093\/nar\/gkl995","article-title":"ArrayExpress\u2013a public database of microarray experiments and gene expression profiles","volume":"35","author":"Parkinson","year":"2007","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/12\/1780\/48924907\/bioinformatics_30_12_1780.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/12\/1780\/48924907\/bioinformatics_30_12_1780.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:42:16Z","timestamp":1674819736000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/12\/1780\/2748164"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,2,25]]},"references-count":5,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2014,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu109","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,2,25]]}}}