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Describing the Orthology Signal in a PPI Network at a Functional, Complex Level

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Bioinformatics Research and Applications (ISBRA 2011)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6674))

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Abstract

In recent work, stable evolutionary signal induced by orthologous proteins has been observed in a Yeast protein-protein interaction (PPI) network. This finding suggests more connected subgraphs of a PPI network to be potential mediators of evolutionary information. Because protein complexes are also likely to be present in such subgraphs, it is interesting to characterize the bias of the orthology signal on the detection of putative protein complexes. To this aim, we propose a novel methodology for quantifying the functionality of the orthology signal in a PPI network at a protein complex level. The methodology performs a differential analysis between the functions of those complexes detected by clustering a PPI network using only proteins with orthologs in another given species, and the functions of complexes detected using the entire network or sub-networks generated by random sampling of proteins. We applied the proposed methodology to a Yeast PPI network using orthology information from a number of different organisms. The results indicated that the proposed method is capable to isolate functional categories that can be clearly attributed to the presence of an evolutionary (orthology) signal and quantify their distribution at a fine-grained protein level.

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Author information

Authors and Affiliations

  1. Institute for Computing and Information Sciences, Radboud University Nijmegen, Postbus 9010, 6500, GL, Nijmegen, The Netherlands

    Pavol Jancura & Elena Marchiori

  2. Department of Medical Microbiology, Radboud University Medical Center, Postbus 9101, 6500, HB, Nijmegen, The Netherlands

    Eleftheria Mavridou

  3. Department of Computer Science, University of Seville, Avda. Reina Mercedes s/n, 41012, Seville, Spain

    Beatriz Pontes

Authors
  1. Pavol Jancura
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  2. Eleftheria Mavridou
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  3. Beatriz Pontes
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  4. Elena Marchiori
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Editor information

Editors and Affiliations

  1. Department of Computer Science and Engineering, Texas A&M University, 77843-3112, College Station, TX, USA

    Jianer Chen

  2. School of Information Science and Engineering, Central South University, 410083, Changsha, China

    Jianxin Wang

  3. Department of Computer Science, Georgia State University, 30303, Atlanta, GA, USA

    Alexander Zelikovsky

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Jancura, P., Mavridou, E., Pontes, B., Marchiori, E. (2011). Describing the Orthology Signal in a PPI Network at a Functional, Complex Level. In: Chen, J., Wang, J., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2011. Lecture Notes in Computer Science(), vol 6674. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21260-4_22

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  • DOI: https://doi.org/10.1007/978-3-642-21260-4_22

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-21259-8

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