Protocol for Genome-scale differential flux analysis (GS-FFA)

Here, we introduce a genome-scale differential flux analysis (GS-DFA) protocol to interrogate the metabolic variances derived from condition-specific gene expression data. It includes scripts for normalizing the gene expression data and integrating it into the HumanGEM framework to create condition-specific models. Moreover, the protocol includes the script for analyzing genome-scale differential flux across the biochemical network, employing condition-specific models. This analytical phase bridges RNA-Seq data with cellular insights, elucidating altered metabolic activities across diverse conditions. The insights can offer valuable perspectives into the intricate metabolic disturbances that play a pivotal role in cellular homeostasis.