Controlling the Effects of External Perturbations on a Gene Regulatory Network Using Proportional-Integral-Derivative Controller.

Gene regulatory networks are biologically robust, which imparts resilience to living systems against most external perturbations affecting them. However, there is a limit to this and disturbances beyond this limit can impart unwanted signalling on one or more master regulators in a network. Certain disturbances may affect the functioning of other constituent genes of the same network. In most cases, this phenomenon can have some effect on the functioning of the living organism. In this investigation, we have proposed a methodology to mitigate the effects of external perturbations on a genetic network using a proportional-integral-derivative controller. The proposed controller has been used to perturb one or more of the other unaffected master regulators such that the most affected gene/s of the network revert to their normal state. The only required condition of such type of manoeuvring is that there should be multiple master regulators in a network. The proposed technique has been experimented on a 10-gene DREAM4 benchmark network and also on a larger 20-gene network, where only downregulation has been considered due to data constraints. Simulation results indicate that the most vulnerable genes can be reverted to their normal expression levels in 10 out of the 16 simulations performed.

Citation

Abhinandan Khan, Goutam Saha, Rajat Kumar Pal. Controlling the Effects of External Perturbations on a Gene Regulatory Network Using Proportional-Integral-Derivative Controller. IEEE/ACM transactions on computational biology and bioinformatics. 2022 May-Jun;19(3):1531-1544

Mesh Tags

PMID: 33206608

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