Wormpath: Searching for molecular interaction networks in Caenorhabditis elegans

Abstract

Background: High-throughput transcriptional profiling using Next-Generation Sequencing (RNA-Seq) or microarray technology have become standard tools in molecular biology. Successful investigations of gene regulatory mechanisms from these data typically employ mathematical models of biological networks. Results: We have developed Wormpath, a software for molecular network discovery which operates on the genetic and physical interaction data of the Wormbase, a comprehensive resource of molecular data on Caenorhabditis elegans. We use Wormpath to show that the insulin/insulin-like growth factor signalling (IIS) pathway responds to UV-induced DNA damage during development. Conclusions: Our software provides highly facilitated access to C. elegans interaction data and is capable of identifying essential molecular networks within a list of differentially expressed genes.