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

Meysman, P.; Sonego, P.; Bianco, L.; Fu, Q.; Ledezma Tejeida, D.; Gama Castro, S.; Liebens, V.; Michiels, J.; Laukens, K.; Marchal, K.; Collado Vides, J.; Engelen, K.A. (2014). COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. NUCLEIC ACIDS RESEARCH, 42 (D1): D649-D653. doi: 10.1093/nar/gkt1086 handle: http://hdl.handle.net/10449/23995

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

Sonego, Paolo;Bianco, Luca;Engelen, Kristof Arthur
2014-01-01

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
Gene expression compendium
Transcriptomics
Microarrays
RNA-seq
Database
Settore BIO/19 - MICROBIOLOGIA GENERALE
2014
Meysman, P.; Sonego, P.; Bianco, L.; Fu, Q.; Ledezma Tejeida, D.; Gama Castro, S.; Liebens, V.; Michiels, J.; Laukens, K.; Marchal, K.; Collado Vides, J.; Engelen, K.A. (2014). COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. NUCLEIC ACIDS RESEARCH, 42 (D1): D649-D653. doi: 10.1093/nar/gkt1086 handle: http://hdl.handle.net/10449/23995
File in questo prodotto:
File Dimensione Formato  
nar-02461-data-e-2013-File001.pdf

accesso aperto

Descrizione: Supplementary information
Licenza: Creative commons
Dimensione 455.5 kB
Formato Adobe PDF
455.5 kB Adobe PDF Visualizza/Apri
2014 NAR Maysman et al.pdf

accesso aperto

Licenza: Creative commons
Dimensione 102.89 kB
Formato Adobe PDF
102.89 kB Adobe PDF Visualizza/Apri

Questo articolo è pubblicato sotto una Licenza Licenza Creative Commons Creative Commons

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10449/23995
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 30
  • ???jsp.display-item.citation.isi??? 30
social impact