Difference between revisions of "Protein-protein interaction databases"
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database here description
Revision as of 02:01, 23 September 2011
|String||database of experimental and predicted interactions; excellent graphics||http://string-db.org/|
|IntAct||derived from literature curation or direct user submissions; tables||http://www.ebi.ac.uk/intact/|
|iHOP||= information hyperlinked over proteins; built by literature mining; results as text clippings||http://www.ihop-net.org/|
|MIPS||Mammalian Protein-Protein Interaction Database (didn't work when tested in Sept '11)||http://mips.helmholtz-muenchen.de/proj/ppi/|
|add another||database here with description here||link|
- collects evidence from genomic Context, high-throughput experiments, conserved coexpression, and text mining
- created by CPR, EMBL, SIB, KU, TUD, and UZH
- latest references: , 
Opinion: easy to use, great graphical interaction map, detailed explanation of evidence
- data from the literature or from direct data depositions by expert curators
- <300k binary interactions in 2011
- developed by the EBI's Proteomics Services Team
- recent reference: Aranda et al. '10
Opinion: The default is an oversized results table (>2 screen widths on a 13"). Use "Change table presets" to compact. Separate columns for links/alias/pubID could be integrated or hover over to make the default table easier on the eye. Overall, the presentation of results seems to be more geared towards bioinformaticians than users with the table full of codes instead of names (Do you know what 9606 is?). Also, no easy species selection and, more importantly, no graphical overview.
- genes and proteins converted into hyperlinks between sentences from PubMed & turned into a conceptual network
- originally developed at CNB-CSIC, authors now at CNIO & MIT
- references: Hoffmann & Valencia 2004 Fernández et al. 2007
Opinion: All information is presented as highlighted text in sentences which makes the information slower to take in than from a structured table and much slower than from a graphical representation. Hypothetical and possibly indirect interactions (A regulates B), non-existent interactions (A does not bind B), and experimental (A co-precipitates with B) are not differentiated. Easy to use, clean species separation.
- The Prince lab present on OWW works on protein-protein interactions.
- OWW's Keating lab also works on protein-protein interactions.
List of protein interaction resources:
Related literature searches