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ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis
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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383876/ https://www.ncbi.nlm.nih.gov/pubmed/25348397 http://dx.doi.org/10.1093/nar/gku1007 |
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author | Veres, Daniel V. Gyurkó, Dávid M. Thaler, Benedek Szalay, Kristóf Z. Fazekas, Dávid Korcsmáros, Tamás Csermely, Peter |
author_facet | Veres, Daniel V. Gyurkó, Dávid M. Thaler, Benedek Szalay, Kristóf Z. Fazekas, Dávid Korcsmáros, Tamás Csermely, Peter |
author_sort | Veres, Daniel V. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4383876 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-43838762015-04-08 ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis Veres, Daniel V. Gyurkó, Dávid M. Thaler, Benedek Szalay, Kristóf Z. Fazekas, Dávid Korcsmáros, Tamás Csermely, Peter Nucleic Acids Res Database Issue 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. Oxford University Press 2015-01-28 2014-10-27 /pmc/articles/PMC4383876/ /pubmed/25348397 http://dx.doi.org/10.1093/nar/gku1007 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Veres, Daniel V. Gyurkó, Dávid M. Thaler, Benedek Szalay, Kristóf Z. Fazekas, Dávid Korcsmáros, Tamás Csermely, Peter ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis |
title | ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis |
title_full | ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis |
title_fullStr | ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis |
title_full_unstemmed | ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis |
title_short | ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis |
title_sort | comppi: a cellular compartment-specific database for protein–protein interaction network analysis |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383876/ https://www.ncbi.nlm.nih.gov/pubmed/25348397 http://dx.doi.org/10.1093/nar/gku1007 |
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