Mining for genes related to choroidal neovascularization based on the shortest path algorithm and protein interaction information

• Published in: Biochimica et biophysica acta Vol. 1860; no. 11; pp. 2740 - 2749
• Main Authors: Zhang, Jian, Suo, Yan, Zhang, Yu-Hang, Zhang, Qing, Chen, XiJia, Xu, Xun, Lu, WenCong
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.11.2016
• Subjects: Algorithms; angiogenesis; BLAST; Choroid - pathology; Choroidal neovascularization; Choroidal Neovascularization - genetics; Dijkstra's algorithm; Disease gene; elderly; eye diseases; gender; genes; genome mining; Humans; obesity; Protein Interaction Maps - genetics; Protein sequence; protein-protein interactions; Protein–protein interaction; Protein sequence; Choroidal neovascularization; Dijkstra's algorithm; BLAST; Protein–protein interaction; Disease gene
• ISSN: 0304-4165; 0006-3002; 1872-8006
• DOI: 10.1016/j.bbagen.2016.03.015

Background: Choroidal neovascularization (CNV) is a serious eye disease that may cause visual loss, especially for older people. Many factors have been proven to induce this disease including age, gender, obesity, and so on. However, until now, we have had limited knowledge on CNV's pathogenic mechanism. Discovering the genes that underlie this disease and performing extensive studies on them can help us to understand how CNV occurs and design effective treatments. Methods: In this study, we designed a computational method to identify novel CNV-related genes in a large protein network constructed using the protein–protein interaction information in STRING. The candidate genes were first extracted from the shortest paths connecting any two known CNV-related genes and then filtered by a permutation test and using knowledge of their linkages to known CNV-related genes. A list of putative CNV-related candidate genes was accessed by our method. These genes are deemed to have strong relationships with CNV. Extensive analyses of several of the putative genes such as ANK1, ITGA4, CD44 and others indicate that they are related to specific biological processes involved in CNV, implying they may be novel CNV-related genes. General significance: The newfound putative CNV-related genes may provide new insights into CNV and help design more effective treatments. This article is part of a Special Issue entitled “System Genetics” Guest Editor: Dr. Yudong Cai and Dr. Tao Huang. •A large network was built using protein–protein interactions of human.•A computational method was proposed to identify CNV-related genes in the network.•A list of putative CNV-related candidate genes was accessed by our method.•Detailed analysis of some putative genes was given in this study.