Protein-protein interaction databases - Revision history

Jakob Suckale: illustration

2011-09-23T11:08:16Z

illustration

←Older revision		Revision as of 11:08, 23 September 2011
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	== [http://thebiogrid.org/ BioGRID] ==		== [http://thebiogrid.org/ BioGRID] ==
		+
		+	[[Image:BioGRID-logo.png\|right]]

	* >400k interactions curated from both high-throughput datasets and primary literature		* >400k interactions curated from both high-throughput datasets and primary literature

2011-09-23T11:04:11Z

database details

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	== [http://thebiogrid.org/ BioGRID] ==		== [http://thebiogrid.org/ BioGRID] ==
		+
		+	* >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.
		+

	== See also ==		== See also ==

2011-09-23T10:54:42Z

overview table

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	\| = information hyperlinked over proteins; built by literature mining; results as text clippings		\| = 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]]
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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.

		+
		+	== [http://thebiogrid.org/ BioGRID] ==

	== See also ==		== See also ==

2011-09-23T10:46:10Z

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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]

-	Wikipedia entry [http://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction protein interaction]	+	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]]

2011-09-23T10:20:34Z

←Older revision		Revision as of 10:20, 23 September 2011
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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]

-	[http://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction ~~Wikipedia entry~~ protein interaction]	+	Wikipedia entry [http://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction protein interaction]

	[[Category:Protein interaction]]		[[Category:Protein interaction]]

2011-09-23T10:20:08Z

2011-09-23T10:18:40Z

←Older revision		Revision as of 10:18, 23 September 2011
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	Lists of protein interaction resources:		Lists of protein interaction resources:
-	* [http://ppi.fli-leibniz.de/jcb_ppi_databases.html huge collection of protein interaction resources]	+	* [http://ppi.fli-leibniz.de/jcb_ppi_databases.html huge collection of protein interaction resources at the FLI]
-	* [http://mips.helmholtz-muenchen.de/proj/ppi/ MIPS (scroll down to other resources]	+	* [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

2011-09-23T10:16:12Z

←Older revision		Revision as of 10:16, 23 September 2011
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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.

-	~~List~~ of protein interaction resources:	+	Lists of protein interaction resources:
		+	* [http://ppi.fli-leibniz.de/jcb_ppi_databases.html huge collection of protein interaction resources]
	* [http://mips.helmholtz-muenchen.de/proj/ppi/ MIPS (scroll down to other resources]		* [http://mips.helmholtz-muenchen.de/proj/ppi/ MIPS (scroll down to other resources]

2011-09-23T10:01:44Z

←Older revision		Revision as of 10:01, 23 September 2011
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	\| http://mips.helmholtz-muenchen.de/proj/ppi/		\| http://mips.helmholtz-muenchen.de/proj/ppi/
	\|-		\|-
-	\| add another ~~database here~~	+	\| add another
-	\| description	+	\| database here with description here
	\| link		\| link
	\|}		\|}

2011-09-23T10:01:17Z

overview table

←Older revision		Revision as of 10:01, 23 September 2011
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	\| http://mips.helmholtz-muenchen.de/proj/ppi/		\| http://mips.helmholtz-muenchen.de/proj/ppi/
	\|-		\|-
-	\| ~~cell 1~~	+	\| add another database here
-	\| ~~cell 2~~	+	\| description
-	\| ~~cell 3~~	+	\| link
-	\|-	+
-	~~\| cell 1~~	+
-	~~\| cell 2~~	+
-	~~\| cell 3~~	+
	\|}		\|}