Authors: Golnaz Taheri; Marzieh Ayati; Limsoon Wong; Changiz Eslahchi
Addresses: School of Mathematics and Computer Science and Center of Excellence in Bioinformatics, College of Science, University of Tehran, Tehran, Iran; Institute for Research in Fundamental Sciences (IPM), Tehran, Iran ' Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA ' Department of Computer Science, National University of Singapore, Singapore ' Department of Computer Science, Shahid Beheshti University G.C., Tehran, Iran
Abstract: Removal of proteins on an essential pathway of a pathogen is expected to prohibit the pathogen from performing a vital function. To disrupt these pathways, we consider a cut set S of simple graph G, where G representing the PPI network of the pathogen. After removing S, if the difference of sizes of two partitions is high, the probability of existence of a functioning pathway is increased. We need to partition the graph into balanced partitions and approximate it with spectral bipartitioning. We consider two scenarios: in the first, we do not have any information on drug targets; in second, we consider information on drug targets. Our databases are E. coli and C. jejuni. In the first scenario, 20% and 17% of proteins in cut of E. coli and C. jejuni are drug targets and in the second scenario 53% and 63% of proteins in cut are drug targets respectively.
Keywords: essential pathways; protein protein interaction; PPI networks; balanced bipartitioning; drug targets; pathogens; drug resistance; co-targeting; bioinformatics; E. coli; C. jejuni.
International Journal of Bioinformatics Research and Applications, 2015 Vol.11 No.1, pp.72 - 89
Available online: 06 Feb 2015 *Full-text access for editors Access for subscribers Purchase this article Comment on this article