Neural networks and temporal gene expression data

Abstract

Temporal gene expression data is of particular interest to systems biology researchers. Such data can be used to create gene networks, where such networks represent the regulatory interactions between genes over time. Reverse engineering gene networks from temporal gene expression data is one of the most important steps in the study of complex biological systems. This paper introduces sensitivity analysis of systematically-perturbed trained neural networks to both select a smaller and more influential subset of genes from a temporal gene expression dataset as well as reverse engineer a gene network from the reduced temporal gene expression data. The methodology was applied to the rat cervical spinal cord development time-course data, and it is demonstrated that the method not only identifies important genes involved in regulatory relationships but also generates candidate gene networks for further experimental study. © Springer-Verlag Berlin Heidelberg 2005.