期刊
BIOINFORMATICS
卷 31, 期 20, 页码 3249-3253出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btv340
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资金
- 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, 2013CB911201, 2010CB912701, 2015CB554406]
- National Natural Science Foundation of China [31170780, 31470809, 31400698]
- National High-Tech Research and Development Program of China [SS2012AA020502, 2011AA02A114]
- International Collaboration Program [2014DFB30020]
- National Megaprojects for Key Infectious Diseases [2013zx10003002]
- NCMIS CAS
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.
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