Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks

  • Phuong Dao
  • Alexander Schönhuth
  • Fereydoun Hormozdiari
  • Iman Hajirasouliha
  • S. Cenk Sahinalp
  • Martin Ester
Conference paper

DOI: 10.1007/978-3-642-04241-6_4

Part of the Lecture Notes in Computer Science book series (LNCS, volume 5724)
Cite this paper as:
Dao P., Schönhuth A., Hormozdiari F., Hajirasouliha I., Sahinalp S.C., Ester M. (2009) Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. In: Salzberg S.L., Warnow T. (eds) Algorithms in Bioinformatics. WABI 2009. Lecture Notes in Computer Science, vol 5724. Springer, Berlin, Heidelberg

Abstract

A current major challenge in systems biology is to compute statistics on biomolecular network motifs, since this can reveal significant systemic differences between organisms. We extend the “color coding” technique to weighted edge networks and apply it to PPI networks where edges are weighted by probabilistic confidence scores, as provided by the STRING database. This is a substantial improvement over the previously available studies on, still heavily noisy, binary-edge-weight data. Following up on such a study, we compute the expected number of occurrences of non-induced subtrees with k ≤ 9 vertices. Beyond the previously reported differences between unicellular and multicellular organisms, we reveal major differences between prokaryotes and unicellular eukaryotes. This establishes, for the first time on a statistically sound data basis, that evolutionary distance can be monitored in terms of elevated systemic arrangements.

Keywords

Biomolecular Network Motifs Color Coding Evolutionary Systems Biology Protein-Protein Interaction Networks 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Phuong Dao
    • 1
  • Alexander Schönhuth
    • 1
  • Fereydoun Hormozdiari
    • 1
  • Iman Hajirasouliha
    • 1
  • S. Cenk Sahinalp
    • 1
  • Martin Ester
    • 1
  1. 1.School of Computing ScienceSimon Fraser UniversityBurnabyCanada

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