Protein-protein interaction databases: Difference between revisions
(database details) |
Victor Tapia (talk | contribs) No edit summary |
||
(13 intermediate revisions by one other user not shown) | |||
Line 5: | Line 5: | ||
|- | |- | ||
| [[Protein-protein interaction databases#String|String]] [[Image:3stars.png]] | | [[Protein-protein interaction databases#String|String]] [[Image:3stars.png]] | ||
| database of experimental and predicted interactions | | database of experimental and predicted interactions; excellent graphics | ||
| http://string-db.org/ | | http://string-db.org/ | ||
|- | |- | ||
| [[Protein-protein interaction databases#IntAct|IntAct]] [[Image:2stars.png]] | | [[Protein-protein interaction databases#IntAct|IntAct]] [[Image:2stars.png]] | ||
| | | derived from literature curation or direct user submissions; tables | ||
| http://www.ebi.ac.uk/intact/ | | http://www.ebi.ac.uk/intact/ | ||
|- | |- | ||
| [[Protein-protein interaction databases#iHOP|iHOP]] | | [[Protein-protein interaction databases#iHOP|iHOP]] [[Image:2stars.png]] | ||
| = information hyperlinked over proteins; built by literature mining | | = information hyperlinked over proteins; built by literature mining; results as text clippings | ||
| http://www.ihop-net.org/ | | http://www.ihop-net.org/ | ||
|- | |||
| [[Protein-protein interaction databases#BioGRID|BioGRID]] [[Image:2stars.png]] | |||
| from literature & high-throughput datasets; best for yeast & A. thaliana | |||
| http://thebiogrid.org/ | |||
|- | |- | ||
| MIPS [[Image:0stars.png]] | | MIPS [[Image:0stars.png]] | ||
Line 20: | Line 24: | ||
| http://mips.helmholtz-muenchen.de/proj/ppi/ | | http://mips.helmholtz-muenchen.de/proj/ppi/ | ||
|- | |- | ||
| | | Mentha | ||
| | | mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way | ||
| | | http://mentha.uniroma2.it/index.php | ||
|- | |- | ||
| | | add another | ||
| | | database here with description here | ||
| | | link | ||
|} | |} | ||
Line 41: | Line 45: | ||
== [http://www.ebi.ac.uk/intact/ IntAct] == | == [http://www.ebi.ac.uk/intact/ IntAct] == | ||
[[Image:Intact-logo.png|right]] | |||
* data from the literature or from direct data depositions by expert curators | * data from the literature or from direct data depositions by expert curators | ||
Line 52: | Line 58: | ||
== [http://www.ihop-net.org/ iHOP] == | == [http://www.ihop-net.org/ iHOP] == | ||
* genes and proteins converted into hyperlinks between sentences from PubMed & turned into a network | [[Image:Ihop logo.gif|right|120px]] | ||
* 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 | * originally developed at CNB-CSIC, authors now at CNIO & MIT | ||
* references: [http://www.nature.com/ng/journal/v36/n7/full/ng0704-664.html Hoffmann & Valencia 2004] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933131/?tool=pubmed Fernández et al. 2007] | * references: [http://www.nature.com/ng/journal/v36/n7/full/ng0704-664.html Hoffmann & Valencia 2004] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933131/?tool=pubmed 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. | |||
== [http://thebiogrid.org/ BioGRID] == | |||
[[Image:BioGRID-logo.png|right]] | |||
* >400k interactions curated from both high-throughput datasets and primary literature | |||
* mostly developed by researchers from Edinburgh, Princeton, and Toronto [http://wiki.thebiogrid.org/doku.php/aboutus#biogrid_team] | |||
* 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] | |||
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. | |||
Line 64: | Line 85: | ||
* OWW's [[Keating:Research|Keating lab]] also works on protein-protein interactions. | * OWW's [[Keating:Research|Keating lab]] also works on protein-protein interactions. | ||
Lists of protein interaction resources: | |||
* [http://mips.helmholtz-muenchen.de/proj/ppi/ MIPS (scroll down to other resources] | * [http://ppi.fli-leibniz.de/jcb_ppi_databases.html huge collection of protein interaction resources at the FLI] | ||
* [http://proteome.wayne.edu/PIDBL.html interaction database list by the Finley lab] | |||
* [http://mips.helmholtz-muenchen.de/proj/ppi/ MIPS (scroll down to other resources)] | |||
Related literature searches | Related literature searches | ||
Line 75: | Line 98: | ||
* [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] | ||
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]] |
Revision as of 03:26, 30 June 2015
Name | Description | Link |
---|---|---|
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/ |
BioGRID | from literature & high-throughput datasets; best for yeast & A. thaliana | http://thebiogrid.org/ |
MIPS | Mammalian Protein-Protein Interaction Database (didn't work when tested in Sept '11) | http://mips.helmholtz-muenchen.de/proj/ppi/ |
Mentha | mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way | http://mentha.uniroma2.it/index.php |
add another | database here with description here | link |
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
- 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.
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
- >400k interactions curated from both high-throughput datasets and primary literature
- mostly developed by researchers from Edinburgh, Princeton, and Toronto [3]
- recent references: The BioGRID Interaction Database: 2011 update, A global protein kinase and phosphatase interaction network in yeast. Breitkreutz et al. '10
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:
- huge collection of protein interaction resources at the FLI
- interaction database list by the Finley lab
- MIPS (scroll down to other resources)
Related literature searches
Recent reviews:
- Databases of protein-protein interactions and complexes. Ooi et al. 2010
- Computational prediction of protein-protein interactions. Skrabanek et al. 2008
- ..the Human Proteotheque Initiative (HuPI). Coulombe et al. 2008
Wikipedia entry protein interaction, interaction prediction