Ontology-and graph-based similarity assessment in biological networks

Authors:
Haiying Wang;Huiru Zheng;Francisco Azuaje
Affiliations:
-;-;-
Venue:
Bioinformatics
Year:
2010

Citing 0
Cited 2

Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease

Journal of Biomedical Informatics
An information theoretic approach to assessing gene-ontology-driven similarity and its application

International Journal of Data Mining and Bioinformatics

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Abstract

Summary: A standard systems-based approach to biomarker and 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, an alternative analysis approach in which the networks are analyzed on a ‘semantic similarity’ space is reported. Such information is extracted from ontology-based functional annotations. We present SimTrek, a Cytoscape plugin for ontology-based similarity assessment in biological networks. Availability: http://rosalind.infj.ulst.ac.uk/SimTrek.html Contact: francisco.azuaje@crp-sante.lu Supplementary information:Supplementary data are available at Bioinformatics online.