Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory
Vivek Kohar1, Danya Gordin1,2,3, Ataur Katebi1,2,3
1The Jackson Laboratory, Bar Harbor, ME 04609, USA.
Bioinformatics (Oxford, England)
|December 6, 2020
Summary
GeneEx is a web-app for simulating gene regulatory circuits (GRCs) using mathematical modeling. It allows exploration of parameter variations, noise, and topology to understand gene expression dynamics.
Area of Science:
- Systems Biology
- Computational Biology
- Molecular Biology
Background:
- Gene regulatory circuits (GRCs) govern gene expression dynamics.
- Understanding GRCs requires robust simulation and analysis tools.
Purpose of the Study:
- To introduce GeneEx, an interactive web-app for simulating and analyzing GRCs.
- To provide a flexible platform for exploring the impact of kinetic parameters, noise, and network topology on GRC behavior.
Main Methods:
- Utilizes Ordinary Differential Equation (ODE)-based mathematical modeling.
- Enables simulation and visualization of GRCs with explicit or ensemble parameter sets.
- Allows modification of simulation parameters, gene expression noise, and network topology.
Main Results:
- Provides insight into the number and stability of attractors for given GRCs.
- Facilitates comparison of experimental gene expression data with simulated data.
- Offers a curated database of circuit motifs and known biological GRCs.
Conclusions:
- GeneEx enables comprehensive investigation of GRCs using a systems biology approach.
- The tool supports hypothesis testing regarding parameter variation, stochasticity, and topological changes in gene expression.
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