ComPPI, a cellular compartment-specific database for protein-protein interaction network analysis

TL;DR

ComPPI is a comprehensive, compartment-specific protein-protein interaction database that enables detailed analysis of cellular localization, interaction likelihood, and biological functions across four species, aiding research in biochemistry, bioinformatics, and medicine.

Contribution

It introduces a novel, integrated database with confidence scoring and filtering capabilities for compartmentalized PPI network analysis across multiple species.

Findings

Enables filtering of biologically unlikely interactions

Predicts compartment-specific biological functions

Provides confidence scores for localizations and interactions

Abstract

Here we present ComPPI, a cellular compartment specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis (http://ComPPI.LinkGroup.hu). ComPPI enables the user to filter biologically unlikely interactions, where the two interacting proteins have no common subcellular localizations and to predict novel properties, such as compartment-specific biological functions. ComPPI is an integrated database covering four species (S. cerevisiae, C. elegans, D. melanogaster and H. sapiens). The compilation of nine protein-protein interaction and eight subcellular localization data sets had four curation steps including a manually built, comprehensive hierarchical structure of more than 1600 subcellular localizations. ComPPI provides confidence scores for protein subcellular localizations and protein-protein interactions. ComPPI has user-friendly search options for individual proteins giving their subcellular localization, their interactions and the likelihood of their interactions considering the subcellular localization of their interacting partners. Download options of search results, whole proteomes, organelle-specific interactomes and subcellular localization data are available on its website. Due to its novel features, ComPPI is useful for the analysis of experimental results in biochemistry and molecular biology, as well as for proteome-wide studies in bioinformatics and network science helping cellular biology, medicine and drug design.