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...

Descripción completa

Guardado en:
Detalles Bibliográficos
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:
R
Q
Acceso en línea:https://doaj.org/article/c0bc9a901f8b496facf0a66514c6e3a3
Etiquetas: Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
id oai:doaj.org-article:c0bc9a901f8b496facf0a66514c6e3a3
record_format dspace
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
_version_ 1718424317070409728