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International Conference on Bioinformatics Research and Development

BIRD 2007: Bioinformatics Research and Development pp 185–198Cite as

Weighted Cohesiveness for Identification of Functional Modules and Their Interconnectivity

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4414))

Abstract

Systems biology offers a holistic perspective where individual proteins are viewed as elements in a network of protein-protein interactions (PPI), in which the proteins have contextual functions within functional modules. In order to facilitate the identification and analysis of such modules, we have previously proposed a Gene Ontology-weighted clustering coefficient for identification of modules in PPI networks and a method, named SWEMODE (Semantic WEights for MODule Elucidation), where this measure is used to identify network modules. Here, we introduce novel aspects of the method that are tested and evaluated. One of the aspects that we consider is to use the k-core graph instead of the original protein-protein interaction graph.Also, by taking the spatial aspect into account, by using the GO cellular component annotation when calculating weighted cohesiveness, we are able to improve the results compared to previous work where only two of the GO aspects (molecular function and biological process) were combined. We here evaluate the predicted modules by calculating their overlap with MIPS functional complexes. In addition, we identify the “most frequent” proteins, i.e. the proteins that most frequently participate in overlapping modules. We also investigate the role of these proteins in the interconnectivity between modules. We find that the majority of identified proteins are involved in the assembly and arrangement of cell structures, such as the cell wall and cell envelope.

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Authors and Affiliations

  1. University of Skövde, School of Humanities and Informatics, Box 408, 54128 Skövde, Sweden

    Zelmina Lubovac, Jonas Gamalielsson & Björn Olsson

  2. Heriot-Watt University, School of Mathematical and Computer Sciences, EH14 4AS Edinburgh, UK

    Zelmina Lubovac, David Corne & Jonas Gamalielsson

Authors
  1. Zelmina Lubovac
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  2. David Corne
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  3. Jonas Gamalielsson
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  4. Björn Olsson
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Sepp Hochreiter Roland Wagner

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© 2007 Springer Berlin Heidelberg

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Lubovac, Z., Corne, D., Gamalielsson, J., Olsson, B. (2007). Weighted Cohesiveness for Identification of Functional Modules and Their Interconnectivity. In: Hochreiter, S., Wagner, R. (eds) Bioinformatics Research and Development. BIRD 2007. Lecture Notes in Computer Science(), vol 4414. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71233-6_15

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  • DOI: https://doi.org/10.1007/978-3-540-71233-6_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-71232-9

  • Online ISBN: 978-3-540-71233-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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