What is ComPPI?

Protein-protein interaction networks are spatially and temporally merged from the results of various experimental and predicting methods. These often ignore localization data, which in turn deteriorates the data quality and its predictive potential.

We present ComPPI, the compartmentalized protein-protein interaction database, which provides qualitative information on the interactions, proteins and their localizations integrated from multiple databases for protein-protein interaction network analysis.

The overlap of the data among various databases can be very low (1), therefore the integration extended with manual curation protocols results in improved data quality.

The subcellular localizations of the interacting proteins are often not taken into consideration, leading to networks with many biologically unlikely interactions. Creating a consensus between the available interaction and localization data further improves the data quality.

ComPPI introduces two novel quantitative scores, the Localization Score and the Interaction Score, which describe the calculated probability of the data correctness.

ComPPI is a novel, integrative, open source database useful for the analysis of experimental results in biochemistry, molecular biology and proteomics as well as for proteome- and interactome-wide studies in bioinformatics and network science helping cellular biology, medicine and drug design.

Quick Statistics

Species Proteins Localizations Interactions
S. cerevisiae 6521 11 423 130 952
C. elegans 20 953 29 281 23 772
D. melanogaster 23 617 31 886 250 854
H. sapiens 74 666 123 225 385 481

Main Features

  • Protein-Protein Interactions

    An integrated dataset of 9 protein-protein interaction databases containing 791 059 interactions.
  • Subcellular Localizations

    An integrated dataset of 8 subcellular localization databases including 195 815 major subcellular localizations.
  • Species

    A comparative assessment of four species: S. cerevisiae, C. elegans, D. melanogaster, H. sapiens
  • 1600+ Gene Ontology Cellular Component Terms

    A hierarchic structure of subcellular localizations using more than 1600 Gene Ontology cellular component terms.
  • Localization and Interaction Scores

    Localization Score for the proteins and Interaction Score for the protein-protein interactions comprising data-quality and interactome-consensus of subcellular localization.
  • Search

    Basic and Advanced Search options for individual proteins with autocomplete function. Filtering is available for species, localization score thresholds of 6 major subcellular localizations and (in the results page) interaction score thresholds of the interacting partners.
  • Download Custom Datasets

    Download options of whole-proteome or organelle-specific interactomes, integrated protein-protein interaction and subcellular localization datasets.


  • 2015/11/23: ComPPI is highly cited!

    ComPPI publication became a highly cited (top 1%) paper ranked by Web-of-Science.

  • 2014/10/09: ComPPI Publication

    ComPPI is accepted for publication in the NAR Database Issue 2015. See the Cite Us page for details.

  • 2014/09/19: ComPPI version 1.1

    ComPPI version 1.1 is released. See the release notes for what's changed.

  • 2014/06/30: ComPPI version 1.0

    The development team is happy to announce the first stable release of ComPPI. See the release notes for what's changed.

  • 2014/06/01: ComPPI Beta

    The first beta of ComPPI is released. All feedback is welcome!

ComPPI is published in Nucleic Acids Research Database Issue 2015