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

Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, S. Cenk Sahinalp, Martin Ester

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationAlgorithms in Bioinformatics - 9th International Workshop, WABI 2009, Proceedings
PublisherSpringer-Verlag
Pages37-48
Number of pages12
ISBN (Print)3642042406, 9783642042409
DOIs
StatePublished - Jan 1 2009
Externally publishedYes
Event9th International Workshop on Algorithms in Bioinformatics, WABI 2009 - Philadelphia, PA, United States
Duration: Sep 12 2009Sep 13 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5724 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other9th International Workshop on Algorithms in Bioinformatics, WABI 2009
CountryUnited States
CityPhiladelphia, PA
Period9/12/099/13/09

Keywords

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

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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    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 Algorithms in Bioinformatics - 9th International Workshop, WABI 2009, Proceedings (pp. 37-48). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5724 LNBI). Springer-Verlag. https://doi.org/10.1007/978-3-642-04241-6_4