User:Jarle Pahr/Protein interaction networks

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://ppi-net.org/

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

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058134#s4

• Uses data from STRING