User:Jarle Pahr/Protein interaction networks

Notes on Protein Interaction Networks (PIN) and relevant databases:

Reactome CytoScape plugin: http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin_4

Jena PPI site: http://ppi.fli-leibniz.de/

http://bioinfow.dep.usal.es/apid/index.htm

http://www.piercenet.com/method/overview-protein-protein-interaction-analysis

Databases

General databases

Biological General Repository for Interaction Datasets (BioGRID): http://thebiogrid.org/

• Covers multiple species
• Download: http://thebiogrid.org/download.php

Protein Interaction Network Analysis (PINA) platform: http://cbg.garvan.unsw.edu.au/pina/interactome.stat.do

• Original publication: http://www.nature.com/nmeth/journal/v6/n1/full/nmeth.1282.html
• Update publication: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244997/
• "Includes a quarterly updated, nonredundant database based on integration of data from six public PPI databases: IntAct3, MINT4, BioGRID5, DIP10, HPRD11 and MIPS MPac" (http://www.nature.com/nmeth/journal/v6/n1/full/nmeth.1282.html)
• Network construction
• Downloadable networks in .sif format based on data from IntAct, BioGRID,MINT,DIP,HPRD and/or MIPS/MPact

http://biology.stackexchange.com/questions/13726/what-are-the-differences-between-hprd-and-biogrid-databases?rq=1

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):

• 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/

• Download: ftp://ftp.ebi.ac.uk/pub/databases/intact/current/

Interologous Interaction Database (I2D): http://ophid.utoronto.ca/ophidv2.204/

• Built by mapping high-throughput (HTP) data between species. Interactions should be considered

predictions.

Single-species databases

Human Protein Reference Database (HPRD): http://www.hprd.org/

• Only manually curated entries
• Requires request submission for download

Domain-specific databases

PDZbase: http://abc.med.cornell.edu/pdzbase

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/

• "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

Organizations

http://ppi-net.org/

http://www.imexconsortium.org/

File formats

Proteomics Standards Initiative-Molecular Interaction (PSI-MI) format: http://www.psidev.info/node/60

• XML-based

http://psidev.sourceforge.net/ http://www.psidev.info/index.php?q=node/31

MIAPE standard: http://www.psidev.info/miape

Networks

Wu et al. 2010. Human functional protein interaction network: http://genomebiology.com/2010/11/5/R53/additional

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
• Uses data from BioGrid, HPRD and IntAct.

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

• Uses data from STRING

Mathivanan et al. BMC Bioinformatics 2006, 7(Suppl 5):S19. An evaluation of human protein-protein interaction data in the public domain. http://www.biomedcentral.com/1471-2105/7/S5/S19/abstract