Reverse engineering gene regulatory network based on complex-valued ordinary differential equation model

• Main Authors: Bin Yang, Wenzheng Bao, Wei Zhang, Haifeng Wang, Chuandong Song, Yuehui Chen, Xiuying Jiang
• Format: Article
• Language: English
• Published: BMC 2021-09-01
• Series: BMC Bioinformatics
• Subjects: Gene regulatory network; Complex-valued ordinary differential equation; Grammar-guided genetic programming; Firefly algorithm
• Online Access: https://doi.org/10.1186/s12859-021-04367-2

Abstract Background The growing researches of molecular biology reveal that complex life phenomena have the ability to demonstrating various types of interactions in the level of genomics. To establish the interactions between genes or proteins and understand the intrinsic mechanisms of biological systems have become an urgent need and study hotspot. Results In order to forecast gene expression data and identify more accurate gene regulatory network, complex-valued version of ordinary differential equation (CVODE) is proposed in this paper. In order to optimize CVODE model, a complex-valued hybrid evolutionary method based on Grammar-guided genetic programming and complex-valued firefly algorithm is presented. Conclusions When tested on three real gene expression datasets from E. coli and Human Cell, the experiment results suggest that CVODE model could improve 20–50% prediction accuracy of gene expression data, which could also infer more true-positive regulatory relationships and less false-positive regulations than ordinary differential equation.