Humess

Humess integrates quantitative transcriptomic analysis with genome-scale metabolic modeling and flux analysis to unveil condition-specific gene signatures and highlight reactions and involved genes based on their metabolic significance.

Key Features:

• Automated pipeline: Uses Snakemake to automatically generate specific human metabolic models from 3'SRP RNA-seq datasets.
• Modified CarveMe integration: Depends on a modified version of CarveMe which uses a top-down approach to build specific metabolic models from a universal model.
• Flux sampling analysis: Performs an optional analysis on generated metabolic models using a sampling procedure.
• Metabolic significance scoring: Highlights reactions and involved genes based on their metabolic significance to offer deeper understanding of transcriptomic data.

Scientific Applications:

• Condition-specific gene signature discovery: Uncovers metabolic phenotypic signatures by informing transcriptomic data analysis with metabolic network modeling.
• Metabolic model generation: Generates specific human metabolic models from 3'SRP RNA-seq data for downstream analysis.
• Multi-layered transcriptomic analysis: Addresses limitations of transcriptomic data alone by incorporating intermodal analysis with metabolic networks.

Methodology:

The pipeline uses Snakemake for workflow management, a modified version of CarveMe with a top-down approach to build specific metabolic models from a universal model, and an optional sampling procedure for metabolic model analysis.