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Clustering with Overlap for Genetic Interaction Networks via Local Search Optimization

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Algorithms in Bioinformatics (WABI 2011)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6833))

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Abstract

Algorithms for detection of modules in genetics interaction networks, while often identifying new models of functional modular organization between genes, have been limited to the output of disjoint, non-overlapping modules, while natural overlapping modules have been observed in biological networks. We present CLOVER, an algorithm for clustering weighted networks into overlapping clusters. We apply this algorithm to the correlation network obtained from a large-scale genetic interaction network of Saccharomyces cerevisiae derived from Synthetic Genetic Arrays (SGA) that covers ~4,500 non-essential genes. We compare CLOVER to previous clustering methods, and demonstrate that genes assigned by our method to multiple clusters known to link distinct biological processes.

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Authors and Affiliations

  1. University of Toronto, Canada

    Joseph Whitney, Judice Koh, Michael Costanzo, Grant Brown, Charles Boone & Michael Brudno

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  1. Joseph Whitney
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  2. Judice Koh
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  3. Michael Costanzo
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  4. Grant Brown
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  5. Charles Boone
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  6. Michael Brudno
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Editor information

Editors and Affiliations

  1. National Center for Biotechnology Information, U.S. National Library of Medicine, 8600 Rockville Pike, 20894, Bethesda, MD, USA

    Teresa M. Przytycka

  2. Institut National de Recherche en Informatique et en Automatique (INRIA) and Université Lyon 1 (UCBL), 43 bd du 11 Novembre 1918, 69622, Villeurbanne cedex, France

    Marie-France Sagot

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Whitney, J., Koh, J., Costanzo, M., Brown, G., Boone, C., Brudno, M. (2011). Clustering with Overlap for Genetic Interaction Networks via Local Search Optimization. In: Przytycka, T.M., Sagot, MF. (eds) Algorithms in Bioinformatics. WABI 2011. Lecture Notes in Computer Science(), vol 6833. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-23038-7_27

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  • DOI: https://doi.org/10.1007/978-3-642-23038-7_27

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-23037-0

  • Online ISBN: 978-3-642-23038-7

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