Decomposition of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing Static and Dynamic Protein Associations

We propose a new method for identifying and representing overlapping functional groups within a protein interaction network. We develop a graph-theoretical framework that enables automatic construction of such representation. The proposed representation helps in understanding the transitions between functional groups and allows for tracking a protein's path through a cascade of functional groups. Therefore, depending on the nature of the network, our representation is capable of elucidating temporal relations between functional groups. We illustrate the effectiveness of our method by applying it to TNFα/NF-κB and pheromone signaling pathways.

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