Cargando…
Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy
Autophagy is a complex cellular process having multiple roles, depending on tissue, physiological, or pathological conditions. Major post-translational regulators of autophagy are well known, however, they have not yet been collected comprehensively. The precise and context-dependent regulation of a...
Autores principales: | , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Taylor & Francis
2015
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4502651/ https://www.ncbi.nlm.nih.gov/pubmed/25635527 http://dx.doi.org/10.4161/15548627.2014.994346 |
_version_ | 1782381245147119616 |
---|---|
author | Türei, Dénes Földvári-Nagy, László Fazekas, Dávid Módos, Dezső Kubisch, János Kadlecsik, Tamás Demeter, Amanda Lenti, Katalin Csermely, Péter Vellai, Tibor Korcsmáros, Tamás |
author_facet | Türei, Dénes Földvári-Nagy, László Fazekas, Dávid Módos, Dezső Kubisch, János Kadlecsik, Tamás Demeter, Amanda Lenti, Katalin Csermely, Péter Vellai, Tibor Korcsmáros, Tamás |
author_sort | Türei, Dénes |
collection | PubMed |
description | Autophagy is a complex cellular process having multiple roles, depending on tissue, physiological, or pathological conditions. Major post-translational regulators of autophagy are well known, however, they have not yet been collected comprehensively. The precise and context-dependent regulation of autophagy necessitates additional regulators, including transcriptional and post-transcriptional components that are listed in various datasets. Prompted by the lack of systems-level autophagy-related information, we manually collected the literature and integrated external resources to gain a high coverage autophagy database. We developed an online resource, Autophagy Regulatory Network (ARN; http://autophagy-regulation.org), to provide an integrated and systems-level database for autophagy research. ARN contains manually curated, imported, and predicted interactions of autophagy components (1,485 proteins with 4,013 interactions) in humans. We listed 413 transcription factors and 386 miRNAs that could regulate autophagy components or their protein regulators. We also connected the above-mentioned autophagy components and regulators with signaling pathways from the SignaLink 2 resource. The user-friendly website of ARN allows researchers without computational background to search, browse, and download the database. The database can be downloaded in SQL, CSV, BioPAX, SBML, PSI-MI, and in a Cytoscape CYS file formats. ARN has the potential to facilitate the experimental validation of novel autophagy components and regulators. In addition, ARN helps the investigation of transcription factors, miRNAs and signaling pathways implicated in the control of the autophagic pathway. The list of such known and predicted regulators could be important in pharmacological attempts against cancer and neurodegenerative diseases. |
format | Online Article Text |
id | pubmed-4502651 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Taylor & Francis |
record_format | MEDLINE/PubMed |
spelling | pubmed-45026512016-01-30 Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy Türei, Dénes Földvári-Nagy, László Fazekas, Dávid Módos, Dezső Kubisch, János Kadlecsik, Tamás Demeter, Amanda Lenti, Katalin Csermely, Péter Vellai, Tibor Korcsmáros, Tamás Autophagy Resource Autophagy is a complex cellular process having multiple roles, depending on tissue, physiological, or pathological conditions. Major post-translational regulators of autophagy are well known, however, they have not yet been collected comprehensively. The precise and context-dependent regulation of autophagy necessitates additional regulators, including transcriptional and post-transcriptional components that are listed in various datasets. Prompted by the lack of systems-level autophagy-related information, we manually collected the literature and integrated external resources to gain a high coverage autophagy database. We developed an online resource, Autophagy Regulatory Network (ARN; http://autophagy-regulation.org), to provide an integrated and systems-level database for autophagy research. ARN contains manually curated, imported, and predicted interactions of autophagy components (1,485 proteins with 4,013 interactions) in humans. We listed 413 transcription factors and 386 miRNAs that could regulate autophagy components or their protein regulators. We also connected the above-mentioned autophagy components and regulators with signaling pathways from the SignaLink 2 resource. The user-friendly website of ARN allows researchers without computational background to search, browse, and download the database. The database can be downloaded in SQL, CSV, BioPAX, SBML, PSI-MI, and in a Cytoscape CYS file formats. ARN has the potential to facilitate the experimental validation of novel autophagy components and regulators. In addition, ARN helps the investigation of transcription factors, miRNAs and signaling pathways implicated in the control of the autophagic pathway. The list of such known and predicted regulators could be important in pharmacological attempts against cancer and neurodegenerative diseases. Taylor & Francis 2015-01-30 /pmc/articles/PMC4502651/ /pubmed/25635527 http://dx.doi.org/10.4161/15548627.2014.994346 Text en © 2015 The Author(s). Published with license by Taylor & Francis Group, LLC http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution-Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The moral rights of the named author(s) have been asserted. |
spellingShingle | Resource Türei, Dénes Földvári-Nagy, László Fazekas, Dávid Módos, Dezső Kubisch, János Kadlecsik, Tamás Demeter, Amanda Lenti, Katalin Csermely, Péter Vellai, Tibor Korcsmáros, Tamás Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy |
title | Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy |
title_full | Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy |
title_fullStr | Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy |
title_full_unstemmed | Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy |
title_short | Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy |
title_sort | autophagy regulatory network — a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy |
topic | Resource |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4502651/ https://www.ncbi.nlm.nih.gov/pubmed/25635527 http://dx.doi.org/10.4161/15548627.2014.994346 |
work_keys_str_mv | AT tureidenes autophagyregulatorynetworkasystemslevelbioinformaticsresourceforstudyingthemechanismandregulationofautophagy AT foldvarinagylaszlo autophagyregulatorynetworkasystemslevelbioinformaticsresourceforstudyingthemechanismandregulationofautophagy AT fazekasdavid autophagyregulatorynetworkasystemslevelbioinformaticsresourceforstudyingthemechanismandregulationofautophagy AT modosdezso autophagyregulatorynetworkasystemslevelbioinformaticsresourceforstudyingthemechanismandregulationofautophagy AT kubischjanos autophagyregulatorynetworkasystemslevelbioinformaticsresourceforstudyingthemechanismandregulationofautophagy AT kadlecsiktamas autophagyregulatorynetworkasystemslevelbioinformaticsresourceforstudyingthemechanismandregulationofautophagy AT demeteramanda autophagyregulatorynetworkasystemslevelbioinformaticsresourceforstudyingthemechanismandregulationofautophagy AT lentikatalin autophagyregulatorynetworkasystemslevelbioinformaticsresourceforstudyingthemechanismandregulationofautophagy AT csermelypeter autophagyregulatorynetworkasystemslevelbioinformaticsresourceforstudyingthemechanismandregulationofautophagy AT vellaitibor autophagyregulatorynetworkasystemslevelbioinformaticsresourceforstudyingthemechanismandregulationofautophagy AT korcsmarostamas autophagyregulatorynetworkasystemslevelbioinformaticsresourceforstudyingthemechanismandregulationofautophagy |