title: COLOMBOS: access port for cross-platform bacterial expression compendia.
abstract: 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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Department of Microbial and Molecular Systems, Katholieke Universiteit Leuven, Heverlee-Leuven, Belgium. kristof.engelen@biw.kuleuven.be
authors.forename: Kristof
authors.initials: K
authors.lastname: Engelen
authors.forename: Qiang
authors.initials: Q
authors.lastname: Fu
authors.forename: Pieter
authors.initials: P
authors.lastname: Meysman
authors.forename: Aminael
authors.initials: A
authors.lastname: Sánchez-Rodríguez
authors.forename: Riet
authors.initials: R
authors.lastname: De Smet
authors.forename: Karen
authors.initials: K
authors.lastname: Lemmens
authors.forename: Ana Carolina
authors.initials: AC
authors.lastname: Fierro
authors.forename: Kathleen
authors.initials: K
authors.lastname: Marchal
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics*; D030541:Databases, Genetic; D004926:Escherichia coli / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D019779:Salmonella enterica / Q000235:genetics*