Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits.
Document Type
Article
Publication Date
6-9-2021
Publication Title
Bioinformatics (Oxford, England)
Keywords
JMG, Databases, Factual, Gene Regulatory Networks, Kinetics, Mobile Applications, Software, Systems Biology
JAX Source
Bioinformatics 2021 Jun 9; 37(9):1327-1329
Volume
37
Issue
9
First Page
1327
Last Page
1329
ISSN
1367-4811
PMID
33279968
DOI
https://doi.org/10.1093/bioinformatics/btaa785
Grant
CA034196, GM128717
Abstract
SUMMARY: GeneEx is an interactive web-app that uses an ODE-based mathematical modeling approach to simulate, visualize and analyze gene regulatory circuits (GRCs) for an explicit kinetic parameter set or for a large ensemble of random parameter sets. GeneEx offers users the freedom to modify many aspects of the simulation such as the parameter ranges, the levels of gene expression noise and the GRC network topology itself. This degree of flexibility allows users to explore a variety of hypotheses by providing insight into the number and stability of attractors for a given GRC. Moreover, users have the option to upload, and subsequently compare, experimental gene expression data to simulated data generated from the analysis of a built or uploaded custom circuit. Finally, GeneEx offers a curated database that contains circuit motifs and known biological GRCs to facilitate further inquiry into these. Overall, GeneEx enables users to investigate the effects of parameter variation, stochasticity and/or topological changes on gene expression for GRCs using a systems-biology approach.
AVAILABILITY AND IMPLEMENTATION: GeneEx is available at https://geneex.jax.org. This web-app is released under the MIT license and is free and open to all users and there is no mandatory login requirement.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Recommended Citation
Kohar V,
Gordin D,
Katebi A,
Levine H,
Onuchic J,
Lu M.
Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits. Bioinformatics 2021 Jun 9; 37(9):1327-1329