KMS Of Academy of mathematics and systems sciences, CAS
| A note on the false discovery rate of novel peptides in proteogenomics | |
Zhang, Kun1,2; Fu, Yan3 ; Zeng, Wen-Feng1,2; He, Kun1,2; Chi, Hao1; Liu, Chao1; Li, Yan-Chang4; Gao, Yuan4; Xu, Ping4; He, Si-Min1
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| 2015-10-15 | |
| 发表期刊 | BIOINFORMATICS
 |
| ISSN | 1367-4803 |
| 卷号 | 31期号:20页码:3249-3253 |
| 摘要 | Motivation: Proteogenomics has been well accepted as a tool to discover novel genes. In most conventional proteogenomic studies, a global false discovery rate is used to filter out false positives for identifying credible novel peptides. However, it has been found that the actual level of false positives in novel peptides is often out of control and behaves differently for different genomes. Results: To quantitatively model this problem, we theoretically analyze the subgroup false discovery rates of annotated and novel peptides. Our analysis shows that the annotation completeness ratio of a genome is the dominant factor influencing the subgroup FDR of novel peptides. Experimental results on two real datasets of Escherichia coli and Mycobacterium tuberculosis support our conjecture. |
| DOI | 10.1093/bioinformatics/btv340 |
| 语种 | 英语 |
| 资助项目 | International S&T Cooperation Program of China[2014DFB30010] ; Strategic Priority Research Program of Chinese Academy of Sciences[XDB13040600] ; National Key Basic Research Program of China[2011CB910600] ; National Key Basic Research Program of China[2013CB911201] ; National Key Basic Research Program of China[2010CB912701] ; National Key Basic Research Program of China[2015CB554406] ; National Natural Science Foundation of China[31170780] ; National Natural Science Foundation of China[31470809] ; National Natural Science Foundation of China[31400698] ; National High-Tech Research and Development Program of China[SS2012AA020502] ; National High-Tech Research and Development Program of China[2011AA02A114] ; International Collaboration Program[2014DFB30020] ; National Megaprojects for Key Infectious Diseases[2013zx10003002] ; NCMIS CAS |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics |
| WOS类目 | Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability |
| WOS记录号 | WOS:000362846600002 |
| 出版者 | OXFORD UNIV PRESS |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.amss.ac.cn/handle/2S8OKBNM/20978 |
| 专题 | 应用数学研究所 |
| 通讯作者 | Fu, Yan |
| 作者单位 | 1.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Key Lab Random Complex Struct & Data Sci, Beijing 100190, Peoples R China 4.Beijing Inst Radiat Med, Natl Engn Res Ctr Prot Drugs, Beijing Proteome Res Ctr, State Key Lab Prote,Natl Ctr Prot Sci Beijing, Beijing 102206, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhang, Kun,Fu, Yan,Zeng, Wen-Feng,et al. A note on the false discovery rate of novel peptides in proteogenomics[J]. BIOINFORMATICS,2015,31(20):3249-3253. |
| APA | Zhang, Kun.,Fu, Yan.,Zeng, Wen-Feng.,He, Kun.,Chi, Hao.,...&He, Si-Min.(2015).A note on the false discovery rate of novel peptides in proteogenomics.BIOINFORMATICS,31(20),3249-3253. |
| MLA | Zhang, Kun,et al."A note on the false discovery rate of novel peptides in proteogenomics".BIOINFORMATICS 31.20(2015):3249-3253. |
| 条目包含的文件 | 条目无相关文件。 | |||||
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