Format

Send to

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

Wormpath: searching for molecular interaction networks in Caenorhabditis elegans.

Author information

1
CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany ; Cologne Center for Genomics, University of Cologne, Cologne, Germany ; Systems Biology of Aging Cologne (SyBACol), University of Cologne, Cologne, Germany.
2
CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany ; Systems Biology of Aging Cologne (SyBACol), University of Cologne, Cologne, Germany ; Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Cologne, Germany ; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.

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.

KEYWORDS:

Gene expression; Molecular interaction networks; Web application; Wormbase

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center