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COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia

BACKGROUND: 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 compend...

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Autores principales: Engelen, Kristof, Fu, Qiang, Meysman, Pieter, Sánchez-Rodríguez, Aminael, De Smet, Riet, Lemmens, Karen, Fierro, Ana Carolina, Marchal, Kathleen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136457/
https://www.ncbi.nlm.nih.gov/pubmed/21779320
http://dx.doi.org/10.1371/journal.pone.0020938
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author Engelen, Kristof
Fu, Qiang
Meysman, Pieter
Sánchez-Rodríguez, Aminael
De Smet, Riet
Lemmens, Karen
Fierro, Ana Carolina
Marchal, Kathleen
author_facet Engelen, Kristof
Fu, Qiang
Meysman, Pieter
Sánchez-Rodríguez, Aminael
De Smet, Riet
Lemmens, Karen
Fierro, Ana Carolina
Marchal, Kathleen
author_sort Engelen, Kristof
collection PubMed
description BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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.
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spelling pubmed-31364572011-07-21 COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia Engelen, Kristof Fu, Qiang Meysman, Pieter Sánchez-Rodríguez, Aminael De Smet, Riet Lemmens, Karen Fierro, Ana Carolina Marchal, Kathleen PLoS One Research Article BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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. Public Library of Science 2011-07-14 /pmc/articles/PMC3136457/ /pubmed/21779320 http://dx.doi.org/10.1371/journal.pone.0020938 Text en Engelen et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Engelen, Kristof
Fu, Qiang
Meysman, Pieter
Sánchez-Rodríguez, Aminael
De Smet, Riet
Lemmens, Karen
Fierro, Ana Carolina
Marchal, Kathleen
COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia
title 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_short COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia
title_sort colombos: access port for cross-platform bacterial expression compendia
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136457/
https://www.ncbi.nlm.nih.gov/pubmed/21779320
http://dx.doi.org/10.1371/journal.pone.0020938
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