title: Mining for genes related to choroidal neovascularization based on the shortest path algorithm and protein interaction information.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Department of Ophthalmology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China; Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai First People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China. Electronic address: natalieeilatan@126.com.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Ophthalmology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China; Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai First People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China. Electronic address: jeanette_suoyan@126.com.
authors.forename: Yan
authors.initials: Y
authors.lastname: Suo
authors.affiliation: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. Electronic address: zhangyh825@163.com.
authors.forename: Yu-Hang
authors.initials: YH
authors.lastname: Zhang
authors.affiliation: School of Life Sciences, Shanghai University, Shanghai 200444, China. Electronic address: qingqing0212@i.shu.edu.cn.
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: School of Life Sciences, Shanghai University, Shanghai 200444, China. Electronic address: cxj371426520@qq.com.
authors.forename: XiJia
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Ophthalmology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China; Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai First People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China. Electronic address: drxuxun@tom.com.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: School of Life Sciences, Shanghai University, Shanghai 200444, China; Department of Chemistry, Shanghai University, Shanghai 200072, China. Electronic address: wclu@shu.edu.cn.
authors.forename: WenCong
authors.initials: W
authors.lastname: Lu
mesh_terms: D000465:Algorithms; D002829:Choroid / Q000473:pathology; D020256:Choroidal Neovascularization / Q000235:genetics*; D006801:Humans; D060066:Protein Interaction Maps / Q000235:genetics*
keywords: BLAST; Choroidal neovascularization; Dijkstra's algorithm; Disease gene; Protein sequence; Protein–protein interaction