Discovering temporal relations in molecular pathways using protein-protein interactions

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

doi:10.1145/974614.974635

Discovering temporal relations in molecular pathways using protein-protein interactions

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

Research output: Contribution to conference › Paper › peer-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 language	English (US)
Pages	150-156
Number of pages	7
DOIs	https://doi.org/10.1145/974614.974635
State	Published - 2004
Event	RECOMB 2004 - Proceedings of the Eight Annual International Conference on Research in Computational Molecular Biology - San Diego, CA., United States Duration: Mar 27 2004 → Mar 31 2004

Conference

Conference	RECOMB 2004 - Proceedings of the Eight Annual International Conference on Research in Computational Molecular Biology
Country/Territory	United States
City	San Diego, CA.
Period	3/27/04 → 3/31/04

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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10.1145/974614.974635

Cite this

Discovering temporal relations in molecular pathways using protein-protein interactions. / Farach-Colton, Martin; Huang, Yang; Woolford, John L.
2004. 150-156 Paper presented at RECOMB 2004 - Proceedings of the Eight Annual International Conference on Research in Computational Molecular Biology, San Diego, CA., United States.

Research output: Contribution to conference › Paper › peer-review

Farach-Colton, M, Huang, Y & Woolford, JL 2004, 'Discovering temporal relations in molecular pathways using protein-protein interactions', Paper presented at RECOMB 2004 - Proceedings of the Eight Annual International Conference on Research in Computational Molecular Biology, San Diego, CA., United States, 3/27/04 - 3/31/04 pp. 150-156. https://doi.org/10.1145/974614.974635

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AB - 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.

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Discovering temporal relations in molecular pathways using protein-protein interactions

Abstract

Conference

Keywords

ASJC Scopus subject areas

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