Difference between revisions of "User:Jarle Pahr/Protein interaction networks"
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Revision as of 06:50, 28 February 2014
Notes on Protein Interaction Networks (PIN) and relevant databases:
Jena PPI site: http://ppi.fli-leibniz.de/
Human Protein Reference Database (HPRD): http://www.hprd.org/
- Only manually curated entries
Biological General Repository for Interaction Datasets (BioGRID): http://thebiogrid.org/
- Covers multiple species
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
Biomolecular Interaction Network Database (BIND)/Biomolecular Object Network Database (BOND):
Interologous Interaction Database (I2D): http://ophid.utoronto.ca/ophidv2.204/
- Built by mapping high-throughput (HTP) data between species. Interactions should be considered predictions.
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/
- "A collection of manually curated high-quality PPI data", includes data only from individually performed experiments.
- Download: http://mips.helmholtz-muenchen.de/proj/ppi/data/mppi.gz
Proteomics Standards Initiative-Molecular Interaction (PSI-MI) format: http://www.psidev.info/node/60
MIAPE standard: http://www.psidev.info/miape
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
- Uses data from BioGrid, HPRD and IntAct.
- Uses data from STRING