Inference of Gene Regulatory Networks Using Time Sliding Comparison and Transcriptional Lagging Time from Time Series Gene Expression Profiles

Abstract

Inference of gene regulatory network from microarray data is one of the most important issues in bioinformatics. Several algorithms have been introduced for this problem, but they cannot give accurate results in case of time series gene expression data. Here, we propose an algorithm that predicts the gene regulatory network more accurately than the previous methods. A new method finds the relationship between a pair of genes by time-shifting the time series data of one gene against another when we compare the patterns of the gene pair. In addition, we increase the accuracy of the prediction method by filtering out the interactions that cannot exist in real biological network. We tested the algorithm to several simulated data which are based on realistic enzyme kinetics system, and evaluated the effectiveness of our algorithm. Results show that the present algorithm significantly improves the accuracy of the inference of gene regulatory network.