User:Jarle Pahr/Protein interaction networks

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

Reactome CytoScape plugin:

Jena PPI site:


General databases

Biological General Repository for Interaction Datasets (BioGRID):

Protein Interaction Network Analysis (PINA) platform:

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


Single-species databases

Human Protein Reference Database (HPRD):

  • Only manually curated entries
  • Requires request submission for download

Domain-specific databases


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:


Wu et al. 2010. Human functional protein interaction network:


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

  • 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.