AutophagyNet

AutophagyNet integrates curated experimental interaction data and structured annotations to map and analyze autophagy regulatory networks across biological contexts.

Key Features:

• Extensive Interaction Database: Contains over 280,000 experimentally verified interactions involving core autophagy proteins and their regulators at protein, transcriptional, and post-transcriptional levels, including potential upstream pathway connections.
• Detailed Annotations: Annotates core autophagy proteins by autophagy type (e.g., mitophagy, xenophagy), stage (initiation, expansion, termination), and subcellular or tissue-specific localization to enable targeted data filtering.
• Customizable Data Access: Provides downloadable data in CSV, BioPAX, and PSI-MI formats for integration with external bioinformatics workflows.
• Data Visualization and Analysis: Supports direct analysis and network visualization within Cytoscape to explore multi-layered regulatory relationships.
• Integration with Omics Data: Designed for use with tissue- or cell type-specific omics datasets such as transcriptomic and proteomic data to contextualize autophagy regulation.

Scientific Applications:

• Disease Research: Facilitates investigation of autophagy malfunction in diseases such as cancer, neurodegenerative disorders, and inflammatory conditions to inform identification of potential therapeutic targets.
• Pathway Analysis: Enables exploration of connections between autophagy pathways and other cellular processes, including innate immune responses and receptor signaling pathways (e.g., BCR, TLR).
• Functional Studies: Supports functional analysis of individual autophagy-related proteins and their roles across different biological contexts.

Methodology:

Builds on the Autophagy Regulatory Network (ARN) and integrates curated experimental interactions with advanced bioinformatics techniques.