COLOMBOS: access port for cross-platform bacterial expression compendia.

<h4>Background</h4>Microarrays are the main technology for large-scale transcriptional gene expression profiling, but the large bodies of data available in public databases are not useful due to the large heterogeneity. There are several initiatives that attempt to bundle these data into...

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Autores principales:	Kristof Engelen, Qiang Fu, Pieter Meysman, Aminael Sánchez-Rodríguez, Riet De Smet, Karen Lemmens, Ana Carolina Fierro, Kathleen Marchal
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c0bc9a901f8b496facf0a66514c6e3a3
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spelling	oai:doaj.org-article:c0bc9a901f8b496facf0a66514c6e3a32021-11-18T06:50:19ZCOLOMBOS: access port for cross-platform bacterial expression compendia.1932-620310.1371/journal.pone.0020938https://doaj.org/article/c0bc9a901f8b496facf0a66514c6e3a32011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21779320/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Microarrays are the main technology for large-scale transcriptional gene expression profiling, but the large bodies of data available in public databases are not useful due to the large heterogeneity. There are several initiatives that attempt to bundle these data into expression compendia, but such resources for bacterial organisms are scarce and limited to integration of experiments from the same platform or to indirect integration of per experiment analysis results.<h4>Methodology/principal findings</h4>We have constructed comprehensive organism-specific cross-platform expression compendia for three bacterial model organisms (Escherichia coli, Bacillus subtilis, and Salmonella enterica serovar Typhimurium) together with an access portal, dubbed COLOMBOS, that not only provides easy access to the compendia, but also includes a suite of tools for exploring, analyzing, and visualizing the data within these compendia. It is freely available at http://bioi.biw.kuleuven.be/colombos. The compendia are unique in directly combining expression information from different microarray platforms and experiments, and we illustrate the potential benefits of this direct integration with a case study: extending the known regulon of the Fur transcription factor of E. coli. The compendia also incorporate extensive annotations for both genes and experimental conditions; these heterogeneous data are functionally integrated in the COLOMBOS analysis tools to interactively browse and query the compendia not only for specific genes or experiments, but also metabolic pathways, transcriptional regulation mechanisms, experimental conditions, biological processes, etc.<h4>Conclusions/significance</h4>We have created cross-platform expression compendia for several bacterial organisms and developed a complementary access port COLOMBOS, that also serves as a convenient expression analysis tool to extract useful biological information. This work is relevant to a large community of microbiologists by facilitating the use of publicly available microarray experiments to support their research.Kristof EngelenQiang FuPieter MeysmanAminael Sánchez-RodríguezRiet De SmetKaren LemmensAna Carolina FierroKathleen MarchalPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 7, p e20938 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kristof Engelen Qiang Fu Pieter Meysman Aminael Sánchez-Rodríguez Riet De Smet Karen Lemmens Ana Carolina Fierro Kathleen Marchal COLOMBOS: access port for cross-platform bacterial expression compendia.
description	<h4>Background</h4>Microarrays are the main technology for large-scale transcriptional gene expression profiling, but the large bodies of data available in public databases are not useful due to the large heterogeneity. There are several initiatives that attempt to bundle these data into expression compendia, but such resources for bacterial organisms are scarce and limited to integration of experiments from the same platform or to indirect integration of per experiment analysis results.<h4>Methodology/principal findings</h4>We have constructed comprehensive organism-specific cross-platform expression compendia for three bacterial model organisms (Escherichia coli, Bacillus subtilis, and Salmonella enterica serovar Typhimurium) together with an access portal, dubbed COLOMBOS, that not only provides easy access to the compendia, but also includes a suite of tools for exploring, analyzing, and visualizing the data within these compendia. It is freely available at http://bioi.biw.kuleuven.be/colombos. The compendia are unique in directly combining expression information from different microarray platforms and experiments, and we illustrate the potential benefits of this direct integration with a case study: extending the known regulon of the Fur transcription factor of E. coli. The compendia also incorporate extensive annotations for both genes and experimental conditions; these heterogeneous data are functionally integrated in the COLOMBOS analysis tools to interactively browse and query the compendia not only for specific genes or experiments, but also metabolic pathways, transcriptional regulation mechanisms, experimental conditions, biological processes, etc.<h4>Conclusions/significance</h4>We have created cross-platform expression compendia for several bacterial organisms and developed a complementary access port COLOMBOS, that also serves as a convenient expression analysis tool to extract useful biological information. This work is relevant to a large community of microbiologists by facilitating the use of publicly available microarray experiments to support their research.
format	article
author	Kristof Engelen Qiang Fu Pieter Meysman Aminael Sánchez-Rodríguez Riet De Smet Karen Lemmens Ana Carolina Fierro Kathleen Marchal
author_facet	Kristof Engelen Qiang Fu Pieter Meysman Aminael Sánchez-Rodríguez Riet De Smet Karen Lemmens Ana Carolina Fierro Kathleen Marchal
author_sort	Kristof Engelen
title	COLOMBOS: access port for cross-platform bacterial expression compendia.
title_short	COLOMBOS: access port for cross-platform bacterial expression compendia.
title_full	COLOMBOS: access port for cross-platform bacterial expression compendia.
title_fullStr	COLOMBOS: access port for cross-platform bacterial expression compendia.
title_full_unstemmed	COLOMBOS: access port for cross-platform bacterial expression compendia.
title_sort	colombos: access port for cross-platform bacterial expression compendia.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/c0bc9a901f8b496facf0a66514c6e3a3
work_keys_str_mv	AT kristofengelen colombosaccessportforcrossplatformbacterialexpressioncompendia AT qiangfu colombosaccessportforcrossplatformbacterialexpressioncompendia AT pietermeysman colombosaccessportforcrossplatformbacterialexpressioncompendia AT aminaelsanchezrodriguez colombosaccessportforcrossplatformbacterialexpressioncompendia AT rietdesmet colombosaccessportforcrossplatformbacterialexpressioncompendia AT karenlemmens colombosaccessportforcrossplatformbacterialexpressioncompendia AT anacarolinafierro colombosaccessportforcrossplatformbacterialexpressioncompendia AT kathleenmarchal colombosaccessportforcrossplatformbacterialexpressioncompendia
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COLOMBOS: access port for cross-platform bacterial expression compendia.

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