MetaPrism

MetaPrism performs joint analysis of metagenomic sequencing data by classifying sequence reads into taxa-specific genes and estimating taxon-linked functional abundances to integrate taxonomical and functional profiling of microbial communities.

Key Features:

• Joint Classification and Abundance Estimation: Classifies sequence reads to taxa-specific genes and estimates their abundances to link taxonomic identities with functional gene profiles.
• Data Tabularization and Visualization: Tabularizes and visualizes abundances of taxa-specific genes for interpretation and comparison of metagenomic profiles.
• Comparative Analysis: Compares gene abundances between groups to identify differences in taxa-specific gene features.
• Predictive Modeling: Builds association and prediction models using joint taxa/gene features to relate metagenomic profiles to clinical outcomes or other phenotypes.

Scientific Applications:

• Immune checkpoint inhibitor therapy biomarker discovery: Demonstrated on a published metagenomic dataset from patients undergoing immune checkpoint inhibitor therapy, highlighting joint taxa/gene features as potential biomarkers for predicting therapeutic responses and supporting translational and personalized medicine research.

Methodology:

Classifying sequence reads to taxa-specific genes, estimating taxa-specific gene abundances, tabularizing and visualizing abundances, comparing gene abundances between groups, and building association and prediction models.