Phenotype prediction tool
Phenotype of Regulatory influences Integrated with Metabolism and Environment (PRIME) is a computational framework to rationally elucidate conditional response phenotypes using integrated networks of regulation and metabolism. PRIME algorithm integrates Environment and Gene Regulatory Influence Network (EGRIN) inferred gene regulatory network (GRN) to the curated genome-scale metabolic network (MN) for TF essentiality and phenotype predictions. Mechanistic inferences associated with the predicted TF essentiality and their network vulnerabilities can be assessed by this approach. PRIME has substantially improved the condition-specific integration of statistically inferred GRN with MN by using gene expression data and environment-specific weights. Specifically, a new 𝜸 factor (Reaction flux influencer) to quantify the magnitude of the influence of a particular TF on genes in a MN has been incorporated, thereby constraining the reaction flux to predict condition-specific phenotypes.