Using large-scale perturbations in gene network reconstruction

Background: Recent analysis of the yeast gene network shows that most genes have few inputs, indicating that enumerative gene reconstruction methods are both useful and computationally feasible. A simple enumerative reconstruction method based on a discrete dynamical system model is used to study how microarray experiments involving modulated global perturbations can be designed to obtain reasonably accurate reconstructions. The method is tested on artificial gene networks with biologically realistic in/out degree characteristics. Results: It was found that a relatively small number of perturbations significantly improve inference accuracy, particularly for low-order inputs of one or two genes. The perturbations themselves should alter the expression level of approximately 50

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Thomas MacCarthy, Andrew Pomiankowski, Robert Seymour
• Keywords: BMCBI 2005, Expression Data, Gene Network, Reconstruction Method