Open Access Highly Accessed Software

Structural Measures for Network Biology Using QuACN

Laurin AJ Mueller1, Karl G Kugler1, Armin Graber1, Frank Emmert-Streib2 and Matthias Dehmer1*

Author Affiliations

1 Institute for Bioinformatics and Translational Research, Department of Biomedical Sciences and Engineering, University for Health Sciences, Medical Informatics and Technology (UMIT), EWZ 1, Hall in Tirol, Austria

2 Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK

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BMC Bioinformatics 2011, 12:492  doi:10.1186/1471-2105-12-492

Published: 24 December 2011

Abstract

Background

Structural measures for networks have been extensively developed, but many of them have not yet demonstrated their sustainably. That means, it remains often unclear whether a particular measure is useful and feasible to solve a particular problem in network biology. Exemplarily, the classification of complex biological networks can be named, for which structural measures are used leading to a minimal classification error. Hence, there is a strong need to provide freely available software packages to calculate and demonstrate the appropriate usage of structural graph measures in network biology.

Results

Here, we discuss topological network descriptors that are implemented in the R-package QuACN and demonstrate their behavior and characteristics by applying them to a set of example graphs. Moreover, we show a representative application to illustrate their capabilities for classifying biological networks. In particular, we infer gene regulatory networks from microarray data and classify them by methods provided by QuACN. Note that QuACN is the first freely available software written in R containing a large number of structural graph measures.

Conclusion

The R package QuACN is under ongoing development and we add promising groups of topological network descriptors continuously. The package can be used to answer intriguing research questions in network biology, e.g., classifying biological data or identifying meaningful biological features, by analyzing the topology of biological networks.