title: COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses.
abstract: COLOMBOS is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. Compared to the previous version it has more than doubled in size, both in terms of species and data available. The manually curated condition annotation has been overhauled as well, giving more complete information about samples' experimental conditions and their differences. Functionality-wise cross-species analyses now enable users to analyse expression data for all species simultaneously, and identify candidate genes with evolutionary conserved expression behaviour. All the expression-based query tools have undergone a substantial improvement, overcoming the limit of enforced co-expression data retrieval and instead enabling the return of more complex patterns of expression behaviour. COLOMBOS is freely available through a web application at http://colombos.net/. The complete database is also accessible via REST API or downloadable as tab-delimited text files.
authors.affiliation: Department of Computational Biology, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Trento (TN) 38010, Italy Department of Biology, University of Padova, Padova (PD) 35121, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Moretto
authors.affiliation: Department of Computational Biology, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Trento (TN) 38010, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Sonego
authors.affiliation: Interuniversity Institute of Bioinformatics Brussels (IB), ULB-VUB, Triomflaan CP 263, B-1050 Brussels, Belgium.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Dierckxsens
authors.affiliation: Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Trento (TN) 38010, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Brilli
authors.affiliation: Department of Computational Biology, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Trento (TN) 38010, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Bianco
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico.
authors.forename: Daniela
authors.initials: D
authors.lastname: Ledezma-Tejeida
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico.
authors.forename: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.affiliation: EMBL-EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.
authors.forename: Marco
authors.initials: M
authors.lastname: Galardini
authors.affiliation: Department of Biology, University of Padova, Padova (PD) 35121, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Romualdi
authors.affiliation: 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.
authors.forename: Kris
authors.initials: K
authors.lastname: Laukens
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico.
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
authors.affiliation: 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.
authors.forename: Pieter
authors.initials: P
authors.lastname: Meysman
authors.affiliation: Department of Computational Biology, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Trento (TN) 38010, Italy kristof.engelen@fmach.it.
authors.forename: Kristof
authors.initials: K
authors.lastname: Engelen
mesh_terms: D001105:Archaea / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D020411:Oligonucleotide Array Sequence Analysis; D017423:Sequence Analysis, RNA; D012984:Software