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论文题目: Determination of Genes Related to Uveitis by Utilization of the Random Walk with Restart Algorithm on a Protein-Protein Interaction Network
英文论文题目: Determination of Genes Related to Uveitis by Utilization of the Random Walk with Restart Algorithm on a Protein-Protein Interaction Network
第一作者: Lu, SH; Yan, Y; Li, Z; Chen, L; Yang, J; Zhang, YH; Wang, SP; Liu, L
英文第一作者: Lu, SH; Yan, Y; Li, Z; Chen, L; Yang, J; Zhang, YH; Wang, SP; Liu, L
联系作者: Liu, L (reprint author), Shanghai Jiao Tong Univ, Sch Med, Ren Ji Hosp, Dept Ophthalmol, Shanghai 200127, Peoples R China.
英文联系作者: Liu, L (reprint author), Shanghai Jiao Tong Univ, Sch Med, Ren Ji Hosp, Dept Ophthalmol, Shanghai 200127, Peoples R China.
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发表年度: 2017
卷: 18
期: 5
页码: 1045
摘要: 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 RandomWalk 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 genes (e.g., CCL4, Jun, and MMP9) are likely to be important for the pathogenesis of uveitis.
英文摘要: 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 RandomWalk 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 genes (e.g., CCL4, Jun, and MMP9) are likely to be important for the pathogenesis of uveitis.
刊物名称: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
英文刊物名称: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
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学科: Biochemistry & Molecular Biology; Chemistry, Multidisciplinary
英文学科: Biochemistry & Molecular Biology; Chemistry, Multidisciplinary
影响因子: 3.226
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论文类别: Article
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