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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
2015-10-15
Source PublicationBIOINFORMATICS
ISSN1367-4803
Volume31Issue:20Pages:3249-3253
AbstractMotivation: 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.
DOI10.1093/bioinformatics/btv340
Language英语
Funding ProjectInternational 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 Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS SubjectBiochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS IDWOS:000362846600002
PublisherOXFORD UNIV PRESS
Citation statistics
Cited Times:15[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/20978
Collection应用数学研究所
Affiliation1.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
Recommended Citation
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.
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