6533b826fe1ef96bd1283f32
RESEARCH PRODUCT
PINCoC: a Co-Clustering based Method to Analyze Protein-Protein Interaction Networks
Clara PizzutiSimona E. Rombosubject
BiclusteringMathematical optimizationBioinformatics network analysisCompact spaceInteraction networkBlock matrixFunction (mathematics)Adjacency matrixGreedy algorithmAlgorithmProtein protein interaction networkMathematicsdescription
Anovel technique to search for functionalmodules in a protein-protein interaction network is presented. The network is represented by the adjacency matrix associated with the undirected graph modelling it. The algorithm introduces the concept of quality of a sub-matrix of the adjacency matrix, and applies a greedy search technique for finding local optimal solutions made of dense submatrices containing the maximum number of ones. An initial random solution, constituted by a single protein, is evolved to search for a locally optimal solution by adding/removing connected proteins that best contribute to improve the quality function. Experimental evaluations carried out on Saccaromyces Cerevisiae proteins show that the algorithm is able to efficiently isolate groups of biologically meaningful proteins corresponding to the most compact sets of interactions.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2007-12-06 |