ERMer

ERMer maps and analyzes the regulatory landscape of Escherichia coli using a graph-database-based serverless platform to identify complex regulatory cascades among genes, transcription factors (TFs), proteins, and small molecules.

Key Features:

• Graph Database Utilization: ERMer uses AWS Neptune to represent regulatory interactions as a graph and to perform deep searches for cascades involving transcription factors (TFs) and small molecules.
• Cloud-Based Architecture: ERMer employs AWS Lambda serverless functions and cloud resources to execute graph queries and scale computation.
• Interactive Visualization: ERMer integrates the G6 graph visualization engine to render and navigate regulatory networks.
• Q&A Module: ERMer provides a graph-query-driven Q&A module that answers complex biological questions via graph traversals.
• Extensible Backend Model: The backend graph schema and data model are designed to be extended as new regulatory data are incorporated.
• Framework Flexibility: The graph-and-cloud framework can be adapted to represent regulatory networks for other organisms or applications.

Scientific Applications:

• Systems Biology and Regulatory Genomics: ERMer supports identification and analysis of multilayer regulatory interactions and cascades in E. coli.
• Gene Expression Regulation: ERMer aids elucidation of regulatory mechanisms among genes, TFs, proteins, and small molecules.
• Microbial Genetics, Synthetic Biology, and Biotechnology: ERMer facilitates mapping of regulatory pathways relevant to discovery and engineering in microbial genetics, synthetic biology, and biotechnology.

Methodology:

ERMer maps E. coli regulatory interactions onto a graph structure stored in AWS Neptune, executes deep graph traversals and queries (including a Q&A module) via serverless AWS Lambda functions, and visualizes networks with the G6 graph visualization engine.