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COLOMBOS v2.0 : an ever expanding collection of bacterial expression compendia

(2014) NUCLEIC ACIDS RESEARCH. 42(D1). p.D649-D653
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
The COLOMBOS database (http://www.colombos.net) features comprehensive organism-specific cross-platform gene expression compendia of several bacterial model organisms and is supported by a fully interactive web portal and an extensive web API. COLOMBOS was originally published in PLoS One, and COLOMBOS v2.0 includes both an update of the expression data, by expanding the previously available compendia and by adding compendia for several new species, and an update of the surrounding functionality, with improved search and visualization options and novel tools for programmatic access to the database. The scope of the database has also been extended to incorporate RNA-seq data in our compendia by a dedicated analysis pipeline. We demonstrate the validity and robustness of this approach by comparing the same RNA samples measured in parallel using both microarrays and RNA-seq. As far as we know, COLOMBOS currently hosts the largest homogenized gene expression compendia available for seven bacterial model organisms.
Keywords
DATABASES, TRANSCRIPTOME, RESOLUTION, ALIGNMENT, NETWORK, GENE-EXPRESSION, RNA-SEQ, ESCHERICHIA-COLI, MICROARRAYS, DATA SETS, IBCN

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Citation

Please use this url to cite or link to this publication:

Chicago
Meysman, Pieter, Paolo Sonego, Luca Bianco, Qiang Fu, Daniela Ledezma-Tejeida, Socorro Gama-Castro, Veerle Liebens, et al. 2014. “COLOMBOS V2.0 : an Ever Expanding Collection of Bacterial Expression Compendia.” Nucleic Acids Research 42 (D1): D649–D653.
APA
Meysman, P., Sonego, P., Bianco, L., Fu, Q., Ledezma-Tejeida, D., Gama-Castro, S., Liebens, V., et al. (2014). COLOMBOS v2.0 : an ever expanding collection of bacterial expression compendia. NUCLEIC ACIDS RESEARCH, 42(D1), D649–D653.
Vancouver
1.
Meysman P, Sonego P, Bianco L, Fu Q, Ledezma-Tejeida D, Gama-Castro S, et al. COLOMBOS v2.0 : an ever expanding collection of bacterial expression compendia. NUCLEIC ACIDS RESEARCH. 2014;42(D1):D649–D653.
MLA
Meysman, Pieter, Paolo Sonego, Luca Bianco, et al. “COLOMBOS V2.0 : an Ever Expanding Collection of Bacterial Expression Compendia.” NUCLEIC ACIDS RESEARCH 42.D1 (2014): D649–D653. Print.
@article{4419847,
  abstract     = {The COLOMBOS database (http://www.colombos.net) features comprehensive organism-specific cross-platform gene expression compendia of several bacterial model organisms and is supported by a fully interactive web portal and an extensive web API. COLOMBOS was originally published in PLoS One, and COLOMBOS v2.0 includes both an update of the expression data, by expanding the previously available compendia and by adding compendia for several new species, and an update of the surrounding functionality, with improved search and visualization options and novel tools for programmatic access to the database. The scope of the database has also been extended to incorporate RNA-seq data in our compendia by a dedicated analysis pipeline. We demonstrate the validity and robustness of this approach by comparing the same RNA samples measured in parallel using both microarrays and RNA-seq. As far as we know, COLOMBOS currently hosts the largest homogenized gene expression compendia available for seven bacterial model organisms.},
  author       = {Meysman, Pieter and Sonego, Paolo and Bianco, Luca and Fu, Qiang and Ledezma-Tejeida, Daniela and Gama-Castro, Socorro and Liebens, Veerle and Michiels, Jan and Laukens, Kris and Marchal, Kathleen and Collado-Vides, Julio and Engelen, Kristof},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {DATABASES,TRANSCRIPTOME,RESOLUTION,ALIGNMENT,NETWORK,GENE-EXPRESSION,RNA-SEQ,ESCHERICHIA-COLI,MICROARRAYS,DATA SETS,IBCN},
  language     = {eng},
  number       = {D1},
  pages        = {D649--D653},
  title        = {COLOMBOS v2.0 : an ever expanding collection of bacterial expression compendia},
  url          = {http://dx.doi.org/10.1093/nar/gkt1086},
  volume       = {42},
  year         = {2014},
}

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