Inference of Large-scale Time-delayed Gene Regulatory Network with Parallel MapReduce Cloud Platform

Overview

Journal Sci Rep

Specialty Science

Date 2018 Dec 14

PMID 30542062

Citations 2

Authors

Bin Yang

Wenzheng Bao

De-Shuang Huang

Yuehui Chen

Affiliations

Soon will be listed here.

Abstract

Inference of gene regulatory network (GRN) is crucial to understand intracellular physiological activity and function of biology. The identification of large-scale GRN has been a difficult and hot topic of system biology in recent years. In order to reduce the computation load for large-scale GRN identification, a parallel algorithm based on restricted gene expression programming (RGEP), namely MPRGEP, is proposed to infer instantaneous and time-delayed regulatory relationships between transcription factors and target genes. In MPRGEP, the structure and parameters of time-delayed S-system (TDSS) model are encoded into one chromosome. An original hybrid optimization approach based on genetic algorithm (GA) and gene expression programming (GEP) is proposed to optimize TDSS model with MapReduce framework. Time-delayed GRNs (TDGRN) with hundreds of genes are utilized to test the performance of MPRGEP. The experiment results reveal that MPRGEP could infer more accurately gene regulatory network than other state-of-art methods, and obtain the convincing speedup.

Citing Articles

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A non-linear reverse-engineering method for inferring genetic regulatory networks.

Wu S, Cui T, Zhang X, Tian T PeerJ. 2020; 8:e9065.

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