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MGclus: Network clustering employing shared neighbors
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholm Bioinformatics Centre, Science for Life Laboratory, Solna, Sweden .
2013 (English)In: Molecular BioSystems, ISSN 1742-206X, Vol. 9, no 7, 1670-1675 p.Article in journal (Refereed) Published
Abstract [en]

Network analysis is an important tool for functional annotation of genes and proteins. A common approach to discern structure in a global network is to infer network clusters, or modules, and assume a functional coherence within each module, which may represent a complex or a pathway. It is however not trivial to define optimal modules. Although many methods have been proposed, it is unclear which methods perform best in general. It seems that most methods produce far from optimal results but in different ways. MGclus is a new algorithm designed to detect modules with a strongly interconnected neighborhood in large scale biological interaction networks. In our benchmarks we found MGclus to outperform other methods when applied to random graphs with varying degree of noise, and to perform equally or better when applied to biological protein interaction networks. MGclus is implemented in Java and utilizes the JGraphT graph library. It has an easy to use command-line interface and is available for download from http://sonnhammer.sbc.su.se/download/software/ MGclus/.

Place, publisher, year, edition, pages
2013. Vol. 9, no 7, 1670-1675 p.
Keyword [en]
Protein-Interaction Networks, Functional Modules, Biological Networks, Complexes, Identification, Algorithm
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-134152DOI: 10.1039/c3mb25473aISI: 000319882200014Scopus ID: 2-s2.0-84878742924OAI: oai:DiVA.org:kth-134152DiVA: diva2:665108
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20131119

Available from: 2013-11-19 Created: 2013-11-18 Last updated: 2013-11-19Bibliographically approved

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