COMPARTMENTS


24573882	COMPARTMENTS: unification and visualization of protein subcellular localization evidence. [PMID: 24573882] Binder JX, Pletscher-Frankild S, Tsafou K, Stolte C, O'Donoghue SI, Schneider R, Jensen LJ. Abstract Information on protein subcellular localization is important to understand the cellular functions of proteins. Currently, such information is manually curated from the literature, obtained from high-throughput microscopy-based screens and predicted from primary sequence. To get a comprehensive view of the localization of a protein, it is thus necessary to consult multiple databases and prediction tools. To address this, we present the COMPARTMENTS resource, which integrates all sources listed above as well as the results of automatic text mining. The resource is automatically kept up to date with source databases, and all localization evidence is mapped onto common protein identifiers and Gene Ontology terms. We further assign confidence scores to the localization evidence to facilitate comparison of different types and sources of evidence. To further improve the comparability, we assign confidence scores based on the type and source of the localization evidence. Finally, we visualize the unified localization evidence for a protein on a schematic cell to provide a simple overview. Database URL: http://compartments.jensenlab.org. Database (Oxford). 2014:2014() \| 298 Citations (from Europe PMC, 2025-03-29)

COMPARTMENTS: unification and visualization of protein subcellular localization evidence. [PMID: 24573882]

Binder JX, Pletscher-Frankild S, Tsafou K, Stolte C, O'Donoghue SI, Schneider R, Jensen LJ.

Information on protein subcellular localization is important to understand the cellular functions of proteins. Currently, such information is manually curated from the literature, obtained from high-throughput microscopy-based screens and predicted from primary sequence. To get a comprehensive view of the localization of a protein, it is thus necessary to consult multiple databases and prediction tools. To address this, we present the COMPARTMENTS resource, which integrates all sources listed above as well as the results of automatic text mining. The resource is automatically kept up to date with source databases, and all localization evidence is mapped onto common protein identifiers and Gene Ontology terms. We further assign confidence scores to the localization evidence to facilitate comparison of different types and sources of evidence. To further improve the comparability, we assign confidence scores based on the type and source of the localization evidence. Finally, we visualize the unified localization evidence for a protein on a schematic cell to provide a simple overview. Database URL: http://compartments.jensenlab.org.

Database (Oxford). 2014:2014() | 298 Citations (from Europe PMC, 2025-03-29)

URL:	http://compartments.jensenlab.org/Search
Full name:	Subcellular localization database
Description:	COMPARTMENTS aims to get a comprehensive view of the localization of a protein.
Year founded:	2014
Last update:	NA
Version:	v1.0
Accessibility:	Accessible
Country/Region:	Germany

Data type:	Protein
Data object:	Animal Fungi Plant
Database category:	Expression
Major species:	Homo sapiens Mus musculus Rattus norvegicus Arabidopsis thaliana Caenorhabditis elegans Drosophila melanogaster
Keywords:	protein subcellular localization

University/Institution:	European Molecular Biology Laboratory
Address:	9117 Heidelberg,Germany
City:	Heidelberg
Province/State:
Country/Region:	Germany
Contact name (PI/Team):	Lars Juhl Jensen
Contact email (PI/Helpdesk):	lars.juhl.jensen@cpr.ku.dk

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Database Commons a catalog of worldwide biological databases