title: Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy.
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.
authors: a Department of Genetics ; Eötvös Loránd University ; Budapest , Hungary.
authors: Dénes
authors: D
authors: Türei
authors: László
authors: L
authors: Földvári-Nagy
authors: Dávid
authors: D
authors: Fazekas
authors: Dezső
authors: D
authors: Módos
authors: János
authors: J
authors: Kubisch
authors: Tamás
authors: T
authors: Kadlecsik
authors: Amanda
authors: A
authors: Demeter
authors: Katalin
authors: K
authors: Lenti
authors: Péter
authors: P
authors: Csermely
authors: Tibor
authors: T
authors: Vellai
authors: Tamás
authors: T
authors: Korcsmáros
mesh_terms: D051017:Apoptosis Regulatory Proteins / Q000378:metabolism; D001343:Autophagy / Q000235:genetics*; D000071186:Beclin-1; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D006801:Humans; D020407:Internet; D008565:Membrane Proteins / Q000378:metabolism; D011485:Protein Binding; D015398:Signal Transduction / Q000235:genetics; D013223:Statistics as Topic
chemical_list: D051017:Apoptosis Regulatory Proteins; C491997:BECN1 protein, human; D000071186:Beclin-1; D008565:Membrane Proteins
keywords: NHR, nuclear hormone receptor; PPI, protein-protein interaction; TFs, transcription factors; autophagy; estrogen receptors; miRNA; miRNA, microRNA; network; protein-protein interactions; regulation; resource; signaling pathway; transcription factors
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