TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.

<h4>Background</h4>As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data.<h4>Methodology</h4>We used a modified version of the Markov clustering algorithm to systematica...

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Autores principales:	Fabrice Lopez, Julien Textoris, Aurélie Bergon, Gilles Didier, Elisabeth Remy, Samuel Granjeaud, Jean Imbert, Catherine Nguyen, Denis Puthier
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d135f9ddce4347efb622e4ac0ce1f4e2
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spelling	oai:doaj.org-article:d135f9ddce4347efb622e4ac0ce1f4e22021-11-25T06:18:06ZTranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.1932-620310.1371/journal.pone.0004001https://doaj.org/article/d135f9ddce4347efb622e4ac0ce1f4e22008-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19104654/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data.<h4>Methodology</h4>We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484). This approach led to the definition of 18,250 transcriptional signatures (TS) that were tested for functional enrichment using the DAVID knowledgebase. Over-representation of functional terms was found in a large proportion of these TS (84%). We developed a JAVA application, TBrowser that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators (http://tagc.univ-mrs.fr/tbrowser/). User can search and analyze TS containing a list of identifiers (gene symbols or AffyIDs) or associated with a set of functional terms.<h4>Conclusions/significance</h4>As proof of principle, TBrowser was used to define breast cancer cell specific genes and to detect chromosomal abnormalities in tumors. Finally, taking advantage of our large collection of transcriptional signatures, we constructed a comprehensive map that summarizes gene-gene co-regulations observed through all the experiments performed on HGU133A Affymetrix platform. We provide evidences that this map can extend our knowledge of cellular signaling pathways.Fabrice LopezJulien TextorisAurélie BergonGilles DidierElisabeth RemySamuel GranjeaudJean ImbertCatherine NguyenDenis PuthierPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 3, Iss 12, p e4001 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Fabrice Lopez Julien Textoris Aurélie Bergon Gilles Didier Elisabeth Remy Samuel Granjeaud Jean Imbert Catherine Nguyen Denis Puthier TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.
description	<h4>Background</h4>As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data.<h4>Methodology</h4>We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484). This approach led to the definition of 18,250 transcriptional signatures (TS) that were tested for functional enrichment using the DAVID knowledgebase. Over-representation of functional terms was found in a large proportion of these TS (84%). We developed a JAVA application, TBrowser that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators (http://tagc.univ-mrs.fr/tbrowser/). User can search and analyze TS containing a list of identifiers (gene symbols or AffyIDs) or associated with a set of functional terms.<h4>Conclusions/significance</h4>As proof of principle, TBrowser was used to define breast cancer cell specific genes and to detect chromosomal abnormalities in tumors. Finally, taking advantage of our large collection of transcriptional signatures, we constructed a comprehensive map that summarizes gene-gene co-regulations observed through all the experiments performed on HGU133A Affymetrix platform. We provide evidences that this map can extend our knowledge of cellular signaling pathways.
format	article
author	Fabrice Lopez Julien Textoris Aurélie Bergon Gilles Didier Elisabeth Remy Samuel Granjeaud Jean Imbert Catherine Nguyen Denis Puthier
author_facet	Fabrice Lopez Julien Textoris Aurélie Bergon Gilles Didier Elisabeth Remy Samuel Granjeaud Jean Imbert Catherine Nguyen Denis Puthier
author_sort	Fabrice Lopez
title	TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.
title_short	TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.
title_full	TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.
title_fullStr	TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.
title_full_unstemmed	TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.
title_sort	transcriptomebrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the gene expression omnibus database.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/d135f9ddce4347efb622e4ac0ce1f4e2
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TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.

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