NetworkTrail—a web service for identifying and visualizing deregulated subnetworks
2013; Oxford University Press; Volume: 29; Issue: 13 Linguagem: Inglês
10.1093/bioinformatics/btt204
ISSN1367-4811
AutoresDaniel Stöckel, Oliver J. Müller, Tim Kehl, Andreas Gerasch, Christina Backes, Alexander Rurainski, Andreas Keller, Michael Kaufmann, Hans‐Peter Lenhof,
Tópico(s)Computational Drug Discovery Methods
ResumoAbstract Summary: The deregulation of biochemical pathways plays a central role in many diseases like cancer or Parkinsons’s disease. In silico tools for calculating these deregulated pathways may help to gain new insights into pathogenic mechanisms and may open novel avenues for therapy stratification in the sense of personalized medicine. Here, we present NetworkTrail, a web service for the detection of deregulated pathways and subgraphs in biological networks. NetworkTrail uses a state-of-the-art integer linear programming-based approach for this task and offers interfaces to the Biological Network Analyzer (BiNA) and Cytoscape Web for visualizing the resulting subnetworks. By providing an accessible interface to otherwise hard-to-use command line tools, the new web service enables non-experts to quickly and reliably carry out this type of network analyses. Availability and implementation: NetworkTrail is a JavaServer Pages-based web service. The algorithm for finding deregulated subnetworks has been implemented in C++. NetworkTrail is available at http://networktrail.bioinf.uni-sb.de/. Contact: dstoeckel@bioinf.uni-sb.de
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