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Integrated Protein Interaction Networks for 11 Microbes

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Research in Computational Molecular Biology (RECOMB 2006)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3909))

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Abstract

We have combined four different types of functional genomic data to create high coverage protein interaction networks for 11 microbes. Our integration algorithm naturally handles statistically dependent predictors and automatically corrects for differing noise levels and data corruption in different evidence sources. We find that many of the predictions in each integrated network hinge on moderate but consistent evidence from multiple sources rather than strong evidence from a single source, yielding novel biology which would be missed if a single data source such as coexpression or coinheritance was used in isolation. In addition to statistical analysis, we demonstrate via case study that these subtle interactions can discover new aspects of even well studied functional modules. Our work represents the largest collection of probabilistic protein interaction networks compiled to date, and our methods can be applied to any sequenced organism and any kind of experimental or computational technique which produces pairwise measures of protein interaction.

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Author information

Authors and Affiliations

  1. Department of Electrical Engineering,  

    Balaji S. Srinivasan

  2. Department of Developmental Biology,  

    Balaji S. Srinivasan & Harley H. McAdams

  3. Department of Computer Science, Stanford University, Stanford, CA, 94305, USA

    Antal F. Novak, Jason A. Flannick & Serafim Batzoglou

Authors
  1. Balaji S. Srinivasan
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  2. Antal F. Novak
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  3. Jason A. Flannick
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  4. Serafim Batzoglou
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  5. Harley H. McAdams
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Editor information

Editors and Affiliations

  1. Georgia Institute of Technology and Università di Padova,  

    Alberto Apostolico

  2. Topic Chairs, P.O. Box

    Concettina Guerra

  3. Center for Molecular Biology and Computer Sciecne Department, Brown University, 115 Waterman St., 02912, Providence, RI, USA

    Sorin Istrail

  4. University of California, San Diego, USA

    Pavel A. Pevzner

  5. Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, 90089-2910, Los Angeles, CA, USA

    Michael Waterman

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© 2006 Springer-Verlag Berlin Heidelberg

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Srinivasan, B.S., Novak, A.F., Flannick, J.A., Batzoglou, S., McAdams, H.H. (2006). Integrated Protein Interaction Networks for 11 Microbes. In: Apostolico, A., Guerra, C., Istrail, S., Pevzner, P.A., Waterman, M. (eds) Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science(), vol 3909. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11732990_1

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  • DOI: https://doi.org/10.1007/11732990_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-33295-4

  • Online ISBN: 978-3-540-33296-1

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