Predicting Variabilities in Cardiac Gene
version 1
Model
Simulation
Analysis
Network Analysis
Knowledge Base
Author:Grieb et. al.
Created:7/21/2016
Updated:2/13/2017
Version:1

Version Description

Description
Gene interactions in cells can be represented by gene regulatory networks. A Boolean network models gene interactions according to rules where gene expression is represented by binary values (on / off or {1, 0}). In reality, however, the gene’s state can have multiple values due to biological properties. Furthermore, the noisy nature of the experimental design results in uncertainty about a state of the gene. Here we present a new Boolean network paradigm to allow intermediate values on the interval [0, 1]. As in the Boolean network, fixed points or attractors of such a model correspond to biological phenotypes or states. We use our new extension of the Boolean network paradigm to model gene expression in first and second heart field lineages which are cardiac progenitor cell populations involved in early vertebrate heart development. By this we are able to predict additional biological phenotypes that the Boolean model alone is not able to identify without utilizing additional biological knowledge. The additional phenotypes predicted by the model were confirmed by published biological experiments. Furthermore, the new method predicts gene expression propensities for modelled but yet to be analyzed genes.

Tags
Heart Field Development, cardiac gene expression, cell differentiation

References
Grieb M, Burkovski A, Str��ng JE, Kraus JM, Gro�� A, Palm G, K��hl M, and Kestler HA.Predicting Variabilities in Cardiac Gene Expression with a Boolean Network Incorporating Uncertainty.PLoS One 2015 Jul 2410; (7) e0131832.pmid:26207376

