Autophagy regulatory network - A systemslevel bioinformatics resource for studying the mechanism and regulation of autophagy

Dénes Türei, Las̈zló Földvári-Nagy, Dávid Fazekas, Dezso Módos, János Kubisch, Tamás Kadlecsik, Amanda Demeter, Katalin Lenti, Péter Csermely, Tibor Vellai, Tamás Korcsmáros

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)155-165
Number of pages11
JournalAutophagy
Volume11
Issue number1
DOIs
Publication statusPublished - Jan 1 2015

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Keywords

  • Autophagy
  • Estrogen receptors
  • MiRNA
  • Network
  • Protein-protein interactions
  • Regulation
  • Resource
  • Signaling pathway
  • Transcription factors

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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