A note on the false discovery rate of novel peptides in proteogenomics

doi:10.1093/bioinformatics/btv340

CORC > 数学与系统科学研究院 > 中国科学院数学与系统科学研究院 > 应用数学研究所

	A note on the false discovery rate of novel peptides in proteogenomics
	Zhang, Kun 1,2; Fu, Yan3 ; Zeng, Wen-Feng 1,2; He, Kun 1,2; Chi, Hao 1; Liu, Chao 1; Li, Yan-Chang 4; Gao, Yuan 4; Xu, Ping 4; He, Si-Min 1
刊名	BIOINFORMATICS
	2015-10-15
卷号	31 期号:20 页码:3249-3253
ISSN号	1367-4803
DOI	10.1093/bioinformatics/btv340
英文摘要	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.
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
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000362846600002
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/20977]
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.