Identification of age-related macular degeneration related genes by applying shortest path algorithm in protein-protein interaction network.
This study attempted to find novel age-related macular degeneration (AMD) related genes based on 36 known AMD genes. The well-known shortest path algorithm, Dijkstra's algorithm, was applied to find the shortest path connecting each pair of known AMD related genes in protein-protein interaction (PPI) network. The genes occurring in any shortest path were considered as candidate AMD related genes. As a result, 125 novel AMD genes were predicted. The further analysis based on betweenness and permutation test indicates that there are 10 genes involved in the formation or development of AMD and may be the actual AMD related genes with high probability. We hope that this contribution would promote the study of age-related macular degeneration and discovery of novel effective treatments.
Department of Ophthalmology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China.
Jian
J
Zhang
State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiaotong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, China.
Min
M
Jiang
State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiaotong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, China.
Fei
F
Yuan
Beijing Genomics Institute, Shenzhen Beishan Industrial Zone, Shenzhen 518083, China.
Kai-Yan
KY
Feng
Institute of Systems Biology, Shanghai University, Shanghai 200444, China.
Yu-Dong
YD
Cai
Department of Ophthalmology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China.
Xun
X
Xu
College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China.
Lei
L
Chen
D000367:Age Factors; D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D020022:Genetic Predisposition to Disease; D006801:Humans; D008268:Macular Degeneration / Q000235:genetics* / Q000473:pathology; D008962:Models, Theoretical; D060066:Protein Interaction Maps / Q000235:genetics*