User:Jarle Pahr/Protein interaction networks: Difference between revisions
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Literature-curated protein interaction datasets: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683745/ | Literature-curated protein interaction datasets: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683745/ | ||
Findings: | |||
* Of all (11858) literature-curated yeast PPIs in BioGRID, more than 75% were supported by only a single publication. | |||
*In a set of 4067 human literature-curated PPIs (http://www.ncbi.nlm.nih.gov/pubmed/16189514/), More than 85% of human PPIs were supported by only a single publication. | |||
*Many available literature-curated PPI datasets are populated widely by PPIs from high-throughput experiments | |||
Addendum: Literature-curated protein interaction datasets: http://www.nature.com/nmeth/journal/v6/n12/full/nmeth1209-934.html | Addendum: Literature-curated protein interaction datasets: http://www.nature.com/nmeth/journal/v6/n12/full/nmeth1209-934.html | ||
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http://ppi-net.org/ | http://ppi-net.org/ | ||
http://www.imexconsortium.org/ | |||
=Bibliography= | =Bibliography= | ||
Revision as of 06:06, 28 February 2014
Notes on Protein Interaction Networks (PIN) and relevant databases:
http://bioinfow.dep.usal.es/apid/index.htm
http://www.piercenet.com/method/overview-protein-protein-interaction-analysis
Databases
Biological General Repository for Interaction Datasets (BioGRID): http://thebiogrid.org/
http://cbg.garvan.unsw.edu.au/pina/interactome.stat.do
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins): http://string-db.org/
- Downloads: http://string-db.org/newstring_cgi/show_download_page.pl?UserId=fw1vitvTA3dy&sessionId=24hG_nRLes36
Human Protein Reference Database (HPRD): http://www.hprd.org/
Biomolecular Interaction Network Database (BIND)/Biomolecular Object Network Database (BOND):
- http://www.ontariogenomics.ca/research/project/62
- http://bond.unleashedinformatics.com/
- http://metadatabase.org/wiki/BIND_-_Biomolecular_Interaction_Network_Database
IntAct: http://www.ebi.ac.uk/intact/
Interologous Interaction Database (I2D): http://ophid.utoronto.ca/ophidv2.204/
- Built by mapping high-throughput (HTP) data between species. Interactions should be considered predictions.
Curated datasets
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245059/
Literature-curated protein interaction datasets: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683745/ Findings:
- Of all (11858) literature-curated yeast PPIs in BioGRID, more than 75% were supported by only a single publication.
- In a set of 4067 human literature-curated PPIs (http://www.ncbi.nlm.nih.gov/pubmed/16189514/), More than 85% of human PPIs were supported by only a single publication.
- Many available literature-curated PPI datasets are populated widely by PPIs from high-throughput experiments
Addendum: Literature-curated protein interaction datasets: http://www.nature.com/nmeth/journal/v6/n12/full/nmeth1209-934.html
Database of Interacting Proteins (DIP): http://dip.doe-mbi.ucla.edu/dip/Main.cgi
- Requires registration
MIPS Mammalian Protein-Protein Interaction Database: http://mips.helmholtz-muenchen.de/proj/ppi/
Organizations
http://www.imexconsortium.org/
Bibliography
http://www.ncbi.nlm.nih.gov/pubmed/20482850
http://genomebiology.com/2010/11/5/R53
A human functional protein interaction network and its application to cancer data analysis: http://genomebiology.com/content/pdf/gb-2010-11-5-r53.pdf
- Network files: http://genomebiology.com/2010/11/5/R53/additional
