Inferring Retinal Degeneration-Related Genes Based on Xgboost

Abstract

Retinal Degeneration (RD) is an inherited retinal disease characterized by degeneration of rods and cones photoreceptor cells and degeneration of retinal pigment epithelial cells. The age of onset and disease progression of RD are related to genes and environment. At present, research has discovered five genes closely related to RD. They are RHO, PDE6B, MERTK, RLBP1, RPGR, and researchers have developed corresponding gene therapy methods. Gene therapy uses vectors to transfer therapeutic genes, genetically modify target cells, and correct or replace disease-causing RD genes. Therefore, identifying the pathogenic genes of RD will play an important role in the development of treatment methods for the disease. However, the traditional methods of identifying RD-related genes are mostly based on animal experiments, and currently only a small number of RD-related genes have been identified. With the increase of biological data, Xgboost is purposed in this article to identify RP-related genes. Xgboost adds a regular term to control the complexity of the model, hence using Xgboost to find out true RD-related genes from complex and massive genes is suitable. The problem of overfitting can be avoided to some extent. To verify the power of Xgboost to identify RD-related genes, we did 10-cross validation and compared with three traditional methods: Random Forest, Back Propagation network, Support Vector Machine. The accuracy of Xgboost is 99.13% and AUC is much higher than other three methods. Therefore, this article can provide technical support for efficient identification of RD-related genes and help researchers have a deeper the understanding of the genetic characteristics of RD.