COLOMBOS: Difference between revisions
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E. coli-centric expression databases | E. coli-centric expression databases | ||
* [[PortEco/expression.porteco.org]] | * [[PortEco/expression.porteco.org]] | ||
* [[ | * [[GenExpDB]] | ||
* [[Many Microbe Microarrays Database (M3D)]] | * [[Many Microbe Microarrays Database (M3D)]] | ||
General repositories | General repositories | ||
Revision as of 08:21, 6 March 2014
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| Link/URL: | |
|---|---|
| What: |
COLlection Of Microarrays for Bacterial OrganismS Gene expression for E. coli and other model bacteria |
| Who: |
Kristof Engelen et al. Department of Computational Biology, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy |
| Updates: | |
| Upcoming events: | |
| Web Services: |
REST services available |
| edit table |
About COLOMBOS
COLOMBOS[1] is a collection of expression data from published microarrays and RNAseq for E. coli, Salmonella enterica, Bacillus subtilis, Streptomyces coelicolor, Pseudomonas aeruginosa, Mycobacterium tuberculosis and Helicobacter pylori. COLOMBOS combines expression analysis across data from different papers, labs, and platforms. A key idea in COLOMBOS is to compare relative expression values to a reference state as sets of "condition contrasts". This should correct for platform-dependent differences between studies.
Content
As of the most recent update published in NAR, COLOMBOS coverage of the E. coli expression data included 3435 microarray or RNAseq samples from 131 experiments.
Using COLOMBOS
Key vocabulary:
- contrast: the difference between a test and reference condition in a particular experiment
- module: saved results of searches for genes, contrasts, or genes and contrasts.
COLOMBOS provides a kind of online workbench where you can create modules by giving lists of genes, experiments, or both. These modules can then be visualized and manipulated in various ways.
Usage examples
Add links to additional pages describing success stories here.
E. coli-centric expression databases
General repositories
Technology
Web Services/API
Discussion
References
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