Autophagy is a highly-conserved catabolic process eliminating dysfunctional cellular
components and invading pathogens. Autophagy malfunction contributes to disorders
such as cancer, neurodegenerative and inflammatory diseases. Understanding autophagy
regulation in health and disease has been the focus of the last decades. We previously
provided an integrated database for autophagy research, the Autophagy Regulatory Network
(ARN). For the last seven years, this resource has been used by thousands of users.
Here, we present a new and upgraded resource, AutophagyNet. It builds on the previous
database but contains major improvements to address user feedback and novel needs
due to the advancement in omics data availability. AutophagyNet contains updated interaction
curation and integration of over 280,000 experimentally verified interactions between
core autophagy proteins and their protein, transcriptional and post-transcriptional
regulators as well as their potential upstream pathway connections. AutophagyNet provides
annotations for each core protein about their role: 1) in different types of autophagy
(mitophagy, xenophagy, etc.); 2) in distinct stages of autophagy (initiation, elongation,
termination, etc); 3) with subcellular and tissue-specific localization. These annotations
can be used to filter the dataset, providing customizable download options tailored
to the user’s needs. The resource is available in various file formats (e.g., CSV,
BioPAX and PSI-MI), and data can be analyzed and visualized directly in Cytoscape.
The multi-layered regulation of autophagy can be analyzed by combining AutophagyNet
with tissue- or cell type-specific using (multi-)omics datasets (e.g. transcriptomic
or proteomic data). The resource is publicly accessible at http://autophagynet.org.Competing
Interest StatementThe authors have declared no competing interest.ARNAutophagy Regulatory
NetworkATGautophagy-related genesBCRB cell receptor pathwayBECN1beclin 1GABARAPgamma-aminobutyric
acid receptor-associated proteinIIPinnate immune pathwaylncRNAlong non-coding RNAmiRNAmicroRNANHRnuclear
hormone receptor pathwayPTMpost-translational modificationRTKreceptor tyrosine kinase
pathwayTCRT cell receptor pathwayTLRToll-like receptor pathway
