Title: PPI network analysis of diabetic retinopathy genes

Authors: Vidhya Gopalakrishnan; Arvind Nambiar; Sukanya Basu; G. Madhuvanthi

Addresses: Faculty of Science and Humanities, Department of Biotechnology, SRMIST, Kattankulathur, Chennai, Tamil Nadu, 603 203, India ' Faculty of Science and Humanities, Department of Biotechnology, SRMIST, Kattankulathur, Chennai, Tamil Nadu, 603 203, India ' Faculty of Science and Humanities, Department of Biotechnology, SRMIST, Kattankulathur, Chennai, Tamil Nadu, 603 203, India ' Faculty of Science and Humanities, Department of Biotechnology, SRMIST, Kattankulathur, Chennai, Tamil Nadu, 603 203, India

Abstract: Diabetic retinopathy (DR) is the leading causes of blindness in many countries. Proteomic studies of DR have discovered a set of genes involved in the disease. In this study, protein protein interaction network (PPIN) of DR proteins were analysed to identify the hub nodes and a PPI network related to retinopathy genes was generated using Cytoscape software. The constructed protein network was analysed using ClusterONE, ClueGO and cytohubba. Among 497 identified candidate proteins, 482 were seen in the main connected component. The topology and functionality of the associated proteins were studied based on centrality parameters such as degree, betweenness and closeness. From the result, two significant clusters were identified which included the experimentally proven five seed proteins. These findings helped in identifying important hub proteins and their direct interacting partners that could be considered as therapeutic biomarkers for treating disease.

Keywords: diabetic retinopathy; PPIN; protein protein interaction network; cytoscape.

DOI: 10.1504/IJCBDD.2020.107892

International Journal of Computational Biology and Drug Design, 2020 Vol.13 No.3, pp.302 - 315

Received: 07 Jan 2019
Accepted: 03 May 2019

Published online: 29 Jun 2020 *

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