User:Jarle Pahr/Protein interaction networks

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Notes on Protein Interaction Networks (PIN) and relevant databases:
Notes on Protein Interaction Networks (PIN) and relevant databases:
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Reactome CytoScape plugin: http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin_4
Jena PPI site: http://ppi.fli-leibniz.de/
Jena PPI site: http://ppi.fli-leibniz.de/

Current revision

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

Contents

Databases

General databases

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

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

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/


Biomolecular Interaction Network Database (BIND)/Biomolecular Object Network Database (BOND):

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.

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/

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


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

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