title: ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis.
abstract: Here we present ComPPI, a cellular compartment-specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis (URL: 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 >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.
authors.affiliation: Department of Medical Chemistry, Semmelweis University, Budapest, Hungary.
authors.forename: Daniel V
authors.identifier: http://orcid.org/0000-0002-2968-0666
authors.initials: DV
authors.lastname: Veres
authors.affiliation: Department of Medical Chemistry, Semmelweis University, Budapest, Hungary.
authors.forename: Dávid M
authors.identifier: http://orcid.org/0000-0002-2997-9799
authors.initials: DM
authors.lastname: Gyurkó
authors.affiliation: Department of Medical Chemistry, Semmelweis University, Budapest, Hungary Faculty of Electrical Engineering and Informatics, Budapest University of Technology and Economics, Budapest, Hungary.
authors.forename: Benedek
authors.initials: B
authors.lastname: Thaler
authors.affiliation: Department of Medical Chemistry, Semmelweis University, Budapest, Hungary.
authors.forename: Kristóf Z
authors.identifier: http://orcid.org/0000-0001-7876-3516
authors.initials: KZ
authors.lastname: Szalay
authors.affiliation: Department of Genetics, Eötvös Loránd University, Budapest, Hungary.
authors.forename: Dávid
authors.initials: D
authors.lastname: Fazekas
authors.affiliation: Department of Genetics, Eötvös Loránd University, Budapest, Hungary TGAC, The Genome Analysis Centre, Norwich, UK Gut Health and Food Safety Programme, Institute of Food Research, Norwich, UK.
authors.forename: Tamás
authors.identifier: http://orcid.org/0000-0003-1717-996X
authors.initials: T
authors.lastname: Korcsmáros
authors.affiliation: Department of Medical Chemistry, Semmelweis University, Budapest, Hungary csermely.peter@med.semmelweis-univ.hu.
authors.forename: Peter
authors.identifier: http://orcid.org/0000-0001-9234-0659
authors.initials: P
authors.lastname: Csermely
mesh_terms: D000818:Animals; D002451:Cell Compartmentation; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D025941:Protein Interaction Mapping; D011506:Proteins / Q000032:analysis / Q000378:metabolism
chemical_list: D011506:Proteins