Title

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.

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