A note on the false discovery rate of novel peptides in proteogenomics.
Bioinformatics
; 31(20): 3249-53, 2015 Oct 15.
Article
em En
| MEDLINE
| ID: mdl-26076724
ABSTRACT
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. CONTACT yfu@amss.ac.cn or xupingghy@gmail.com or smhe@ict.ac.cn SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Temas:
Geral
Base de dados:
MEDLINE
Assunto principal:
Peptídeos
/
Proteômica
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2015
Tipo de documento:
Article