Bacteriome
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| What: |
An integrated protein interaction database for E. coli. Bacteriome features a high quality functional interaction dataset of E. coli proteins togther with experimental datasets generated through tandem affinity purification screens. |
| Who: |
Parkinson Lab together with Andrew Emili and Jack Greenblatt |
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About Bacteriome
Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase [1].
Content
Bacteriome offers access to two types of network: 1) A network of functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework [2].
2) Two networks of experimentally derived protein-protein interactions - a 'core' network consisting of interactions deemed to be of 'high quality'; and an 'extended' network which extends the 'core' network by including interactions for which experimental evidence is less strong [3]. Note these experimental datasets do not correlate precisely with the experimental datasets described in the PLoS Biology reference. The datasets described in the PLoS Biology paper were subjected to a seperate and unrelated Bayesian integration exercise.
The Bacteriome website, offers the user the ability to select groups of proteins on the basis of simple text searches (e.g. 'kinase'), domian composition, functional and evolutionary relationships. Selected proteins may then be visualised within the context of known interactions using the two datasets described above. In addition, the website offers the use the ability to explore the modular organization of the E. coli proteome through taking a complex-centric view of proteins.
Alternatively the interaction datasets are also available for download without restriction.
In addition to visualizing proteins through their functional relationships, proteins may additionbally be visualized in the context of their domain architecture or through their phylogenetic profiles.
Using Bacteriome
Browsing
Searching
Usage examples
Add links to additional pages describing success stories here.
Technology
Web Services/API
Discussion
References
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- ↑ Su, C et al. (2008) Bacteriome.org--an integrated protein interaction database for E. coli. Nucleic Acids Res. 36 D632-6 PubMed
- ↑ Peregrín-Alvarez, JM et al. (2009) The Modular Organization of Protein Interactions in Escherichia coli. PLoS Comput. Biol. 5 e1000523 PubMed
- ↑ Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
External Links
[link Bacteriome] URL:link