MetaQUBIC

MetaQUBIC integrates paired metagenomic and metatranscriptomic datasets and applies biclustering to detect co-expressed cross-species gene modules for functional analysis of microbial communities.

Key Features:

• Integrated Data Analysis: Combines metagenomic (DNA) and metatranscriptomic (RNA) data to capture both gene presence and active gene expression profiles.
• Biclustering-Based Approach: Employs biclustering algorithms to identify co-expressed gene modules across different species within a microbiome.
• Comprehensive Hybrid Expression Matrix: Generates a hybrid gene expression matrix applied to 735 paired DNA and RNA human gut samples encompassing over 2.3 million cross-species genes.
• Functional Enrichment Analysis: Performs functional enrichment on detected gene modules and identified 155 enriched modules in the human gut dataset.

Scientific Applications:

• Microbial community structure and function: Characterizes gene modules to relate genetic potential and expression patterns to community functional organization.
• Host–microbiome interaction studies: Enables interrogation of gene expression modules relevant to interactions between microbiomes and host environments.
• Biomarker discovery for health and disease: Supports identification of gene modules and expression signatures associated with health or disease states.

Methodology:

Processes paired metagenomic and metatranscriptomic datasets to construct a hybrid gene expression matrix; integrates DNA and RNA data; applies biclustering algorithms to detect co-expressed gene modules across species; and conducts functional enrichment analysis of detected modules.