User:Jarle Pahr/Protein interaction networks

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*Original publication:
*Original publication:
*Update publication:
*Update publication:
*Network construction
*Downloadable networks in .sif format based on data from IntAct, BioGRID,MINT,DIP,HPRD and/or MIPS/MPact

Revision as of 10:13, 28 February 2014

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

Jena PPI site:



Human Protein Reference Database (HPRD):

  • Only manually curated entries

Biological General Repository for Interaction Datasets (BioGRID):

Protein Interaction Network Analysis (PINA):

STRING (Search Tool for the Retrieval of Interacting Genes/Proteins):

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


Interologous Interaction Database (I2D):

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

Curated datasets

Literature-curated protein interaction datasets: 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 (, 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:

Database of Interacting Proteins (DIP):

  • Requires registration

MIPS Mammalian Protein-Protein Interaction Database:


File formats

Proteomics Standards Initiative-Molecular Interaction (PSI-MI) format:

  • XML-based

MIAPE standard:


A human functional protein interaction network and its application to cancer data analysis:

  • Uses data from STRING
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