Haiying Wang1, Huiru Zheng1 and Francisco Azuaje2
1 Computer Science Research Institute, School of Computing and Mathematics, University of Ulster, UK.
2Laboratory of Cardiovascular Research, Public Research Centre for Health (CRP-Sante), L-1150, Luxembourg.
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A standard systems-based approach to biomarker (or drug target) discovery consists of placing putative biomarkers in the context of a network of biological interactions, followed by different “guilt-by-association” analyses. The latter is typically done based on network structural features. Here we report an alternative analysis approach in which the networks are analyzed on a “semantic similarity” space. Such information is extracted from ontology-based functional annotations. We present SimTrek, a Cytoscape plugin for ontology-based similarity assessment of biological networks.
New features in V1.2:
New features in V1.3:
If you use this software in your research please cite:
Wang H, Zheng H, Azuaje F (2010) Ontology- and graph-based similarity assessment in biological networks, Bioinformatics.