Detecting shifts in gene regulatory networks during time-course experiments at single-time-point temporal resolution

J Bioinform Comput Biol. 2015 Oct;13(5):1543002. doi: 10.1142/S0219720015430027. Epub 2015 Sep 30.

Abstract

Comprehensively understanding the dynamics of biological systems is one of the greatest challenges in biology. Vastly improved biological technologies have provided vast amounts of information that must be understood by bioinformatics and systems biology researchers. Gene regulations have been frequently modeled by ordinary differential equations or graphical models based on time-course gene expression profiles. The state-of-the-art computational approaches for analyzing gene regulations assume that their models are same throughout time-course experiments. However, these approaches cannot easily analyze transient changes at a time point, such as diauxic shift. We propose a score that analyzes the gene regulations at each time point. The score is based on the information gains of information criterion values. The method detects the shifts in gene regulatory networks (GRNs) during time-course experiments with single-time-point resolution. The effectiveness of the method is evaluated on the diauxic shift from glucose to lactose in Escherichia coli. Gene regulation shifts were detected at two time points: the first corresponding to the time at which the growth of E. coli ceased and the second corresponding to the end of the experiment, when the nutrient sources (glucose and lactose) had become exhausted. According to these results, the proposed score and method can appropriately detect the time of gene regulation shifts. The method based on the proposed score provides a new tool for analyzing dynamic biological systems. Because the score value indicates the strength of gene regulation at each time point in a gene expression profile, it can potentially infer hidden GRNs from time-course experiments.

Keywords: Gene regulatory network; diauxic shift; network dynamics; time-course.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Computational Biology / methods*
  • Computer Graphics
  • Escherichia coli / genetics
  • Escherichia coli / growth & development
  • Escherichia coli / metabolism
  • Gene Expression Profiling
  • Gene Regulatory Networks*
  • Genome, Bacterial
  • Glucose / metabolism
  • Humans
  • Lactose / metabolism
  • Markov Chains
  • Mice
  • Models, Genetic
  • Systems Biology
  • Time Factors

Substances

  • Glucose
  • Lactose