Predicting Phenotype from Genotype Through Automatically Composed Petri Nets
Year: 2012
Type: preprint
Abstract: We describe a modular modelling approach permitting curation, updating, and distributed development of modules through joined community effort overcoming the problem of keeping a combinatorially exploding number of monolithic models up to date. For this purpose, the effects of genes and their mutated alleles on downstream components are modeled by composable, metadata-containing Petri net models organized in a database with version control, accessible through a web interface. Gene modules can be coupled to protein modules through mRNA modules by specific interfaces designed for the automatic, database-assisted composition. Automatically assembled executable models may then consider cell type-specific gene expression patterns and the resulting protein concentrations. Gene modules and allelic interference modules may represent effects of gene mutation and predict their pleiotropic consequences or uncover complex genotype/phenotype relationships. Forward and reverse engineered modules are fully compatible.
Source: arXiv (Cornell University)
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2953198760