Discovering temporal relations in molecular pathways using protein-protein interactions

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 proteinprotein 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. Categories and Subject Descriptors J.3 [Computer Applications]: Life and Medical Sciences General Terms Algorithms, Experimentation Keywords Interval graphs, probe interval graphs, vertex ordering, protein-protein interaction, molecular pathways, ribosoma...

• Type: Conference
• Year: 2004
• Where: RECOMB
• Authors: Martin Farach-Colton, Yang Huang, John L. L. Woolford
• Keywords: Computational Biology, Interval Graphs, Molecular Pathways, RECOMB 2004, Sciences General Terms