Protein-protein interaction databases

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| [[Protein-protein interaction databases#String|String]] [[Image:3stars.png]]
| [[Protein-protein interaction databases#String|String]] [[Image:3stars.png]]
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| database of experimental and predicted interactions
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| database of experimental and predicted interactions; excellent graphics
| http://string-db.org/
| http://string-db.org/
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| [[Protein-protein interaction databases#IntAct|IntAct]] [[Image:2stars.png]]
| [[Protein-protein interaction databases#IntAct|IntAct]] [[Image:2stars.png]]
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| interactions derived from literature curation or direct user submissions
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| derived from literature curation or direct user submissions; tables
| http://www.ebi.ac.uk/intact/
| http://www.ebi.ac.uk/intact/
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| [[Protein-protein interaction databases#iHOP|iHOP]] [[Image:2stars.png]]
| [[Protein-protein interaction databases#iHOP|iHOP]] [[Image:2stars.png]]
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| = information hyperlinked over proteins; built by literature mining
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| = information hyperlinked over proteins; built by literature mining; results as text clippings
| http://www.ihop-net.org/
| http://www.ihop-net.org/
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|-
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| [[Protein-protein interaction databases#BioGRID|BioGRID]] [[Image:2stars.png]]
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| from literature & high-throughput datasets; best for yeast & A. thaliana
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| http://thebiogrid.org/
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| MIPS [[Image:0stars.png]]
| MIPS [[Image:0stars.png]]
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| http://mips.helmholtz-muenchen.de/proj/ppi/
| http://mips.helmholtz-muenchen.de/proj/ppi/
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| database here with description here
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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.
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.
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== [http://thebiogrid.org/ BioGRID] ==
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[[Image:BioGRID-logo.png|right]]
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* >400k interactions curated from both high-throughput datasets and primary literature
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* mostly developed by researchers from Edinburgh, Princeton, and Toronto [http://wiki.thebiogrid.org/doku.php/aboutus#biogrid_team]
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* recent references: [http://www.ncbi.nlm.nih.gov/pubmed/21071413 The BioGRID Interaction Database: 2011 update], [http://www.ncbi.nlm.nih.gov/pubmed/20489023 A global protein kinase and phosphatase interaction network in yeast. Breitkreutz et al. '10]
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Opinion: Good interface but generally fewer hits than other databases for mammalian genes. This is probably because this database contains mainly yeast protein interactions where it is very strong. It is currently being extended towards other metazoans. Nice representation of evidence as high & low throughput with reference and description.
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* OWW's [[Keating:Research|Keating lab]] also works on protein-protein interactions.
* OWW's [[Keating:Research|Keating lab]] also works on protein-protein interactions.
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List of protein interaction resources:
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Lists of protein interaction resources:
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* [http://mips.helmholtz-muenchen.de/proj/ppi/ MIPS (scroll down to other resources]
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* [http://ppi.fli-leibniz.de/jcb_ppi_databases.html huge collection of protein interaction resources at the FLI]
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* [http://proteome.wayne.edu/PIDBL.html interaction database list by the Finley lab]
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* [http://mips.helmholtz-muenchen.de/proj/ppi/ MIPS (scroll down to other resources)]
Related literature searches
Related literature searches
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* [http://www.ncbi.nlm.nih.gov/pubmed/18443628 ..the Human Proteotheque Initiative (HuPI). Coulombe et al. 2008]
* [http://www.ncbi.nlm.nih.gov/pubmed/18443628 ..the Human Proteotheque Initiative (HuPI). Coulombe et al. 2008]
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Wikipedia entry [http://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction protein interaction], [http://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction_prediction interaction prediction]
[[Category:Protein interaction]]
[[Category:Protein interaction]]

Current revision

Name Description Link
String Image:3stars.png database of experimental and predicted interactions; excellent graphics http://string-db.org/
IntAct Image:2stars.png derived from literature curation or direct user submissions; tables http://www.ebi.ac.uk/intact/
iHOP Image:2stars.png = information hyperlinked over proteins; built by literature mining; results as text clippings http://www.ihop-net.org/
BioGRID Image:2stars.png from literature & high-throughput datasets; best for yeast & A. thaliana http://thebiogrid.org/
MIPS Image:0stars.png 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

Contents

String

  • collects evidence from genomic Context, high-throughput experiments, conserved coexpression, and text mining
  • created by CPR, EMBL, SIB, KU, TUD, and UZH
  • latest references: [1], [2]

Opinion: easy to use, great graphical interaction map, detailed explanation of evidence


IntAct

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.


iHOP

  • 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.


BioGRID

Opinion: Good interface but generally fewer hits than other databases for mammalian genes. This is probably because this database contains mainly yeast protein interactions where it is very strong. It is currently being extended towards other metazoans. Nice representation of evidence as high & low throughput with reference and description.


See also

On OpenWetWare

  • The Prince lab present on OWW works on protein-protein interactions.
  • OWW's Keating lab also works on protein-protein interactions.

Lists of protein interaction resources:

Related literature searches

  • search PubMed for MeSH term Protein Interaction Mapping [4], major topic [5], and reviews only [6]

Recent reviews:

Wikipedia entry protein interaction, interaction prediction

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