Gene Regulatory Identification Based on the Novel Hybrid Time-Delayed Method

Abstract

Gene regulatory network (GRN) inference with biology data is a difficult and serious issue in the field of system biology. In order to detect the direct associations of GRN more accurately, a novel two-step GRN inference technique based on the time-delayed correlation coefficient (TDCC) and time-delayed complex-valued S-system model (TDCVSS) is proposed. First, a TDCC algorithm is utilized to construct an initial network. Second, a TDCVSS model is utilized to prune the network topology in order to delete false-positive regulatory relationships for each target gene. The complex-valued restricted additive tree and complex-valued differential evolution are proposed to approximate the optimal TDCVSS model. Finally, the overall network could be inferred by integrating the regulations of all target genes. Two real gene expression datasets from E. coli and S. cerevisiae gene networks are utilized to evaluate the performances of our proposed two-step GRN inference algorithm. The results demonstrated that the proposed algorithm could infer GRN more correct than classical methods and time-delayed methods.

Keywords: S-system model; complex-valued; gene regulatory network; system biology; time-delayed.