Discovering temporal relations in molecular pathways using protein-protein interactions

Martin Farach-Colton, Yang Huang, John L. Woolford

    Research output: Contribution to conferencePaperpeer-review

    Abstract

    The availability of large-scale protein-protein interaction data provides us with many opportunities to study molecular pathways involving proteins. In this paper we propose to mine temporal relations in molecular pathways by protein-protein interaction data. In particular, we model the assembly pathways of protein complexes with interval graphs and determine the temporal order of joining the pathway for proteins by ordering the vertices in the interaction graph. We develop a tool called XRONOS to perform such a computation. We then apply XRONOS to the ribosome assembly pathway and present validation results for the obtained ordering. The results are promising and show the potential usage for XRONOS in the study of molecular pathways.

    Original languageEnglish (US)
    Pages150-156
    Number of pages7
    DOIs
    StatePublished - 2004
    EventRECOMB 2004 - Proceedings of the Eight Annual International Conference on Research in Computational Molecular Biology - San Diego, CA., United States
    Duration: Mar 27 2004Mar 31 2004

    Conference

    ConferenceRECOMB 2004 - Proceedings of the Eight Annual International Conference on Research in Computational Molecular Biology
    Country/TerritoryUnited States
    CitySan Diego, CA.
    Period3/27/043/31/04

    Keywords

    • Interval graphs
    • Molecular pathways
    • Probe interval graphs
    • Protein-protein interaction
    • Ribosomal assembly pathway
    • Vertex ordering

    ASJC Scopus subject areas

    • General Computer Science
    • General Biochemistry, Genetics and Molecular Biology

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