文章基本信息

标题：Inference of Large-scale Time-delayed Gene Regulatory Network with Parallel MapReduce Cloud Platform
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作者：Bin Yang ; Wenzheng Bao ; De-Shuang Huang 等
期刊名称：Scientific Reports
电子版ISSN：2045-2322
出版年度：2018
卷号：8
期号：1
页码：17787
DOI：10.1038/s41598-018-36180-y
语种：English
出版社：Springer Nature
摘要：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.