Pathway Analysis and Multi-Omics Data Visualization through AgileBioCyc

AgileBioCyc is a collection of Agile BioFoundry organism-specific Pathway/Genome Databases (PGDB) where each PGDB has been curated to include all the engineered pathways that have been designed for the organism. AgileBioCyc is intended to be used to interpret multi-omics measurements in the context of the metabolic and regulatory pathways of the host organism. AgileBioCyc provides a number of tools to aid in the analysis and visualization of mechanisms of action, including Smart Tables and the OmicsDashboard.

AgileBioCyc MultiOmics Analysis and Visualization tools

  • SmartTables are used to link proteomics, metabolomics, and flux statistical analyses to knowledge about proteins, metabolites, and reactions that have been captured in the PGDB.
  • OmicsDashboard is a tool for visualizing multiomics data. It facilitates a rapid user survey of how all cellular systems are responding to a given stimulus. It enables the user to quickly find and understand the response of genes within one or more specific systems of interest, and to gauge the relative activity levels of different cellular systems. The dashboard also enables a user to compare the expression levels of a cellular system with those of its known regulators.
  • Many other multiomics data analysis and visualization tools

AgileBioCyc Metabolic, Regulatory and Genome Browsers

  • Constraint-based Metabolic Reconstruction and Analysis Tools: Flux Balance Analysis (FBA) is a computational method for simulating an organism’s metabolic network. Metabolic models based on FBA depict a steady-state condition of a cell. Among the components of the simulation are the biochemical reactions in the organism’s metabolic network, the metabolites utilized by the organism as nutrients, the compounds secreted by the organism, and the biomass metabolites synthesized by the metabolic network. The nutrients are the inputs to the metabolic machinery, and the secretions and biomass metabolites are the outputs of that machinery.
  • Regulatory network analysis and visualization: The Regulatory Overview allows you to visually analyze the regulatory relationships between genes for a specific organism.
  • Genome Browser: The genome browser can be used to examine one replicon (chromosome or plasmid) at a time. Its tracks capability can be used to visualize high-throughput datasets in a genome context.