FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model
文献类型：期刊论文
| 作者 | Wang, Mingjun1,2; Zhao, Xing-Ming3; Takemoto, Kazuhiro4; Xu, Haisong1,2; Li, Yuan1,2; Akutsu, Tatsuya5; Song, Jiangning1,2,5,6 |
| 刊名 | PLOS ONE
 |
| 出版日期 | 2012-08-24 |
| 卷号 | 7期号:8页码:e43847 |
| 英文摘要 | Single amino acid variants (SAVs) are the most abundant form of known genetic variations associated with human disease. Successful prediction of the functional impact of SAVs from sequences can thus lead to an improved understanding of the underlying mechanisms of why a SAV may be associated with certain disease. In this work, we constructed a high-quality structural dataset that contained 679 high-quality protein structures with 2,048 SAVs by collecting the human genetic variant data from multiple resources and dividing them into two categories, i.e., disease-associated and neutral variants. We built a two-stage random forest (RF) model, termed as FunSAV, to predict the functional effect of SAVs by combining sequence, structure and residue-contact network features with other additional features that were not explored in previous studies. Importantly, a two-step feature selection procedure was proposed to select the most important and informative features that contribute to the prediction of disease association of SAVs. In cross-validation experiments on the benchmark dataset, FunSAV achieved a good prediction performance with the area under the curve (AUC) of 0.882, which is competitive with and in some cases better than other existing tools including SIFT, SNAP, Polyphen2, PANTHER, nsSNPAnalyzer and PhD-SNP. The sourcecodes of FunSAV and the datasets can be downloaded at http://sunflower.kuicr.kyoto-u.ac.jp/similar to sjn/FunSAV. |
| WOS标题词 | Science & Technology |
| 类目[WOS] | Multidisciplinary Sciences |
| 研究领域[WOS] | Science & Technology - Other Topics |
| 关键词[WOS] | PROTEIN SECONDARY STRUCTURE ; SUPPORT VECTOR MACHINES ; NUCLEOTIDE POLYMORPHISMS ; EVOLUTIONARY INFORMATION ; CONTACT PREDICTION ; GENOME SEQUENCE ; HUMAN GENES ; DISEASE ; MUTATIONS ; SUBSTITUTIONS |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000308225500109 |
| 公开日期 | 2012-10-12 |
| 源URL | [http://124.16.173.210/handle/312001/275]  |
| 专题 | 天津工业生物技术研究所_结构生物信息学和整合系统生物学实验室 宋江宁_期刊论文 |
| 作者单位 | 1.Chinese Acad Sci, Natl Engn Lab Ind Enzymes, Tianjin Inst Ind Biotechnol, Tianjin, Peoples R China 2.Chinese Acad Sci, Key Lab Syst Microbial Biotechnol, Tianjin Inst Ind Biotechnol, Tianjin, Peoples R China 3.Tongji Univ, Dept Comp Sci, Sch Elect & Informat Engn, Shanghai 200092, Peoples R China 4.Kyushu Inst Technol, Dept Biosci & Bioinformat, Iizuka, Fukuoka, Japan 5.Kyoto Univ, Bioinformat Ctr, Inst Chem Res, Uji, Kyoto, Japan 6.Monash Univ, Dept Biochem & Mol Biol, Melbourne, Vic 3004, Australia |
| 推荐引用方式 GB/T 7714 | Wang, Mingjun,Zhao, Xing-Ming,Takemoto, Kazuhiro,et al. FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model[J]. PLOS ONE,2012,7(8):e43847. |
| APA | Wang, Mingjun.,Zhao, Xing-Ming.,Takemoto, Kazuhiro.,Xu, Haisong.,Li, Yuan.,...&Song, Jiangning.(2012).FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model.PLOS ONE,7(8),e43847. |
| MLA | Wang, Mingjun,et al."FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model".PLOS ONE 7.8(2012):e43847. |
入库方式： OAI收割
来源：天津工业生物技术研究所
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