COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.
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.
Department of Mathematics and Computer Science, University of Antwerp, B-2020 Antwerp, Belgium, Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, B-2650 Edegem, Belgium, Department of Computational Biology, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Trento (TN) 38010, Italy, Department of Microbial and Molecular Sciences, KU Leuven, Leuven B-3001, Belgium, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico, Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent 9052, Belgium and Department of Information Technology, IMinds, Ghent University, Gent 9052, Belgium.
Pieter
P
Meysman
Paolo
P
Sonego
Luca
L
Bianco
Qiang
Q
Fu
Daniela
D
Ledezma-Tejeida
Socorro
S
Gama-Castro
Veerle
V
Liebens
Jan
J
Michiels
Kris
K
Laukens
Kathleen
K
Marchal
Julio
J
Collado-Vides
Kristof
K
Engelen
D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D030541:Databases, Genetic; D015870:Gene Expression; D020869:Gene Expression Profiling; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D017423:Sequence Analysis, RNA