Title: Identification of protein complexes in protein-protein interaction networks by core-attachment approach incorporating gene expression profile
Authors: Seketoulie Keretsu; Rosy Sarmah
Addresses: Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur, Sonitpur, Assam 784028, India ' Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur, Sonitpur, Assam 784028, India
Abstract: Due to the advancement in Proteomic technologies, bulk data of protein-protein interactions (PPI) are available which give researchers in bioinformatics the opportunity to explore and understand biological properties and structure from a networking perspective. Identification of protein complexes is a challenge that has emerged as an attraction to researchers particularly in computational biology. Various computational approaches were developed to identify protein complexes in PPI networks. In this paper, we give a new method based on the core-attachment approach with incorporation of gene expression data known as core-attachment with gene (CAG) expression to identify protein complexes in PPI networks. Experiment results support that our method CAG can detect protein complexes effectively. Validation by biological information, namely co-localisation and gene ontology semantic similarity score reveals that the complexes predicted by our method has high biological relevance. We also give a comparison of our method with four other popular methods in the field.
Keywords: gene expression analysis; protein clustering; protein complexes; protein-protein interaction networks.
DOI: 10.1504/IJBRA.2017.087382
International Journal of Bioinformatics Research and Applications, 2017 Vol.13 No.4, pp.313 - 328
Received: 18 Dec 2015
Accepted: 07 Aug 2016
Published online: 14 Oct 2017 *