Determination of Genes Related to Uveitis by Utilization of the Random Walk with Restart Algorithm on a Protein-Protein Interaction Network

International Journal of Molecular Sciences
Shiheng LuLin Liu

Abstract

Uveitis, defined as inflammation of the uveal tract, may cause blindness in both young and middle-aged people. Approximately 10-15% of blindness in the West is caused by uveitis. Therefore, a comprehensive investigation to determine the disease pathogenesis is urgent, as it will thus be possible to design effective treatments. Identification of the disease genes that cause uveitis is an important requirement to achieve this goal. To begin to answer this question, in this study, a computational method was proposed to identify novel uveitis-related genes. This method was executed on a large protein-protein interaction network and employed a popular ranking algorithm, the Random Walk with Restart (RWR) algorithm. To improve the utility of the method, a permutation test and a procedure for selecting core genes were added, which helped to exclude false discoveries and select the most important candidate genes. The five-fold cross-validation was adopted to evaluate the method, yielding the average F1-measure of 0.189. In addition, we compared our method with a classic GBA-based method to further indicate its utility. Based on our method, 56 putative genes were chosen for further assessment. We have determined that several of these ge...Continue Reading

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Citations

Feb 15, 2018·International Journal of Molecular Sciences·Quan Zou, Wenying He
Jun 9, 2020·Briefings in Bioinformatics·Jing TangFeng Zhu
Jun 1, 2018·BioMed Research International·YuanYuan LuoZhen Li
May 27, 2020·Computational and Mathematical Methods in Medicine·Haiyan LiangXiaolin Zhang
Aug 3, 2018·Molecular Therapy. Methods & Clinical Development·Lei ChenYu-Dong Cai

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Methods Mentioned

BETA
transfection

Software Mentioned

Matlab
R
Ensembl
STRING
RWR

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