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NucEnvDB: A Database of Nuclear Envelope Proteins and Their Interactions
The nuclear envelope (NE) is a double-membrane system surrounding the nucleus of eukaryotic cells. A large number of proteins are localized in the NE, performing a wide variety of functions, from the bidirectional exchange of molecules between the cytoplasm and the nucleus to chromatin tethering, ge...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9861991/ https://www.ncbi.nlm.nih.gov/pubmed/36676869 http://dx.doi.org/10.3390/membranes13010062 |
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author | Baltoumas, Fotis A. Sofras, Dimitrios Apostolakou, Avgi E. Litou, Zoi I. Iconomidou, Vassiliki A. |
author_facet | Baltoumas, Fotis A. Sofras, Dimitrios Apostolakou, Avgi E. Litou, Zoi I. Iconomidou, Vassiliki A. |
author_sort | Baltoumas, Fotis A. |
collection | PubMed |
description | The nuclear envelope (NE) is a double-membrane system surrounding the nucleus of eukaryotic cells. A large number of proteins are localized in the NE, performing a wide variety of functions, from the bidirectional exchange of molecules between the cytoplasm and the nucleus to chromatin tethering, genome organization, regulation of signaling cascades, and many others. Despite its importance, several aspects of the NE, including its protein–protein interactions, remain understudied. In this work, we present NucEnvDB, a publicly available database of NE proteins and their interactions. Each database entry contains useful annotation including a description of its position in the NE, its interactions with other proteins, and cross-references to major biological repositories. In addition, the database provides users with a number of visualization and analysis tools, including the ability to construct and visualize protein–protein interaction networks and perform functional enrichment analysis for clusters of NE proteins and their interaction partners. The capabilities of NucEnvDB and its analysis tools are showcased by two informative case studies, exploring protein–protein interactions in Hutchinson–Gilford progeria and during SARS-CoV-2 infection at the level of the nuclear envelope. |
format | Online Article Text |
id | pubmed-9861991 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-98619912023-01-22 NucEnvDB: A Database of Nuclear Envelope Proteins and Their Interactions Baltoumas, Fotis A. Sofras, Dimitrios Apostolakou, Avgi E. Litou, Zoi I. Iconomidou, Vassiliki A. Membranes (Basel) Article The nuclear envelope (NE) is a double-membrane system surrounding the nucleus of eukaryotic cells. A large number of proteins are localized in the NE, performing a wide variety of functions, from the bidirectional exchange of molecules between the cytoplasm and the nucleus to chromatin tethering, genome organization, regulation of signaling cascades, and many others. Despite its importance, several aspects of the NE, including its protein–protein interactions, remain understudied. In this work, we present NucEnvDB, a publicly available database of NE proteins and their interactions. Each database entry contains useful annotation including a description of its position in the NE, its interactions with other proteins, and cross-references to major biological repositories. In addition, the database provides users with a number of visualization and analysis tools, including the ability to construct and visualize protein–protein interaction networks and perform functional enrichment analysis for clusters of NE proteins and their interaction partners. The capabilities of NucEnvDB and its analysis tools are showcased by two informative case studies, exploring protein–protein interactions in Hutchinson–Gilford progeria and during SARS-CoV-2 infection at the level of the nuclear envelope. MDPI 2023-01-03 /pmc/articles/PMC9861991/ /pubmed/36676869 http://dx.doi.org/10.3390/membranes13010062 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Baltoumas, Fotis A. Sofras, Dimitrios Apostolakou, Avgi E. Litou, Zoi I. Iconomidou, Vassiliki A. NucEnvDB: A Database of Nuclear Envelope Proteins and Their Interactions |
title | NucEnvDB: A Database of Nuclear Envelope Proteins and Their Interactions |
title_full | NucEnvDB: A Database of Nuclear Envelope Proteins and Their Interactions |
title_fullStr | NucEnvDB: A Database of Nuclear Envelope Proteins and Their Interactions |
title_full_unstemmed | NucEnvDB: A Database of Nuclear Envelope Proteins and Their Interactions |
title_short | NucEnvDB: A Database of Nuclear Envelope Proteins and Their Interactions |
title_sort | nucenvdb: a database of nuclear envelope proteins and their interactions |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9861991/ https://www.ncbi.nlm.nih.gov/pubmed/36676869 http://dx.doi.org/10.3390/membranes13010062 |
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