Pattern discovery in breast cancer specific protein interaction network.

Abstract

The interest in indentifying novel biomarkers for early stage breast cancer (BRCA) detection has become grown significantly in recent years. From a view of network biology, one of the emerging themes today is to re-characterize a protein's biological functions in its molecular network. Although many methods have been presented, including network-based gene ranking for molecular biomarker discovery, and graph clustering for functional module discovery, it is still hard to find systems-level properties hidden in disease specific molecular networks. We reconstructed BRCA-related protein interaction network by using BRCA-associated genes/proteins as seeds, and expanding them in an integrated protein interaction database. We further developed a computational framework based on Ant Colony Optimization to rank network nodes. The task of ranking nodes is represented as the problem of finding optimal density distributions of "ant colonies" on all nodes of the network. Our results revealed some interesting systems-level pattern in BRCA-related protein interaction network.