Wormpath: searching for molecular interaction networks in Caenorhabditis elegans

Source Code Biol Med. 2015 Apr 2;10:5. doi: 10.1186/s13029-015-0034-6. eCollection 2015.


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.

Keywords: Gene expression; Molecular interaction networks; Web application; Wormbase.