Discovering temporal relations in molecular pathways using protein-protein interactions

Authors:
Martin Farach-Colton;Yang Huang;John L. L. Woolford
Affiliations:
Rutgers University, Piscataway, NJ;Rutgers University, Piscataway, NJ;Carnegie Mellon University, Pittsburgh, PA
Venue:
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Year:
2004

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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.