ArticleNucleic acids research2014
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- A computational exploration of resilience and evolvability of protein-protein interaction networks.Communications biology · 2021Article
- BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus.BMC bioinformatics · 2019Article
- A comprehensive evaluation of module detection methods for gene expression data.Nature communications · 2018Article
- Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.Current protocols in bioinformatics · 2018Article
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- Multiplex methods provide effective integration of multi-omic data in genome-scale models.BMC bioinformatics · 2016Article
- COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses.Nucleic acids research · 2016Article
- RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.Nucleic acids research · 2016Article
- VESPUCCI: Exploring Patterns of Gene Expression in Grapevine.Frontiers in plant science · 2016Article
- Practical Approaches for Mining Frequent Patterns in Molecular Datasets.Bioinformatics and biology insights · 2016Review
- Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.PLoS computational biology · 2015Article
- Regulation of flavonol content and composition in (Syrah×Pinot Noir) mature grapes: integration of transcriptional profiling and metabolic quantitative trait locus analyses.Journal of experimental botany · 2015Article
- New candidate genes for the fine regulation of the colour of grapes.Journal of experimental botany · 2015Article
- Genome-scale identification and characterization of moonlighting proteins.Biology direct · 2014Article
- Mutation rate plasticity in rifampicin resistance depends on Escherichia coli cell-cell interactions.Nature communications · 2014Article
- Structural properties of prokaryotic promoter regions correlate with functional features.PloS one · 2014Article
- Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12.Database : the journal of biological databases and curation · 2014Article
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Authors and funding
12 authors.
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No grant is acknowledged in the PubMed record.
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.
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