MPA_Pathway_Tool

MPA_Pathway_Tool maps genes, transcripts, or proteins from microbial community multi‑omics data to user‑defined biological pathways with optional taxonomic constraints to enable taxonomic and functional characterization across environments such as the human gut and biogas plants.

Key Features:

• Pathway-Creator: Enables creation of custom-defined pathways and incorporation of specific taxonomic constraints for pathway definitions.
• Pathway-Calculator: Maps microbial community data from multiple measurements onto selected pathways and generates visualizations of pathway-level results.
• Gene/Transcript/Protein assignment: Assigns genes, transcripts, or proteins to biological pathways to link molecular entities to functional modules.
• Reuse and customization of metabolic pathways: Supports reuse of existing metabolic pathways while allowing creation of new, customized pathway definitions.

Scientific Applications:

• Multi-omics pathway analysis: Linking metagenomic, metatranscriptomic, and metaproteomic data to biological pathways to assess functional activity.
• Taxonomic-functional profiling: Characterizing functional roles of individual species and entire microbial communities using taxonomic constraints.
• Environmental microbiology: Comparative functional analysis of microbial communities in environments such as the human gut and biogas plants.

Methodology:

Implemented using Java and ReactJS; supports reuse of existing metabolic pathways and creation of customized pathways; maps community measurements to pathways applying optional taxonomic constraints.