Discovery and revision of Arabidopsis genes by proteogenomics

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 52, 2008, Pages 21034-21038

  Castellana, Natalie E ^a   Payne, Samuel H ^b   Shen, Zhouxin ^b   Stanke, Mario ^c   Bafna, Vineet ^a   Briggs, Steven P ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Institute for Microbiology and Genetics   (Germany)

Author keywords

Annotation; Genomics; Proteomics

Indexed keywords

ARABIDOPSIS PROTEIN;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; GENOMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ISOLATION; PROTEOMICS; RNA SPLICING; RNA TRANSLATION; TANDEM MASS SPECTROMETRY;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; GENOME, PLANT; MODELS, GENETIC; PROTEOME; PROTEOMICS; SOFTWARE;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 58549101102     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0811066106     Document Type: Article

References (16)

1. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254.
2. Lin MF, et al. (2007) Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res 17:1823-1836.
3. Brent MR (2008) Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat Rev Genet 9:62-73.
4. Baerenfaller K, et al. (2008) Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320:938-941.
5. Brunner E, et al. (2007) A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol 25:576-583.
6. Tanner S, et al. (2007) Improving gene annotation using peptide mass spectrometry. Genome Res 17:231-239.
7. Savidor A, et al. (2006) Expressed peptide tags: An additional layer of data for genome annotation. J Proteome Res 5:3048-3058.
8. Gupta N, et al. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation. Genome Res 17:1362-1377.
9. Fermin D, et al. (2006) Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol 7:R35.
10. Desiere F, et al. (2005) Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol 6:R9.
11. Stanke M, et al. (2006) AUGUSTUS: Ab initio prediction of alternative transcripts. Nucleic Acids Res 34:W435-9.
12. Jiang B, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431:163-167.
13. Hanada K, Zhang X, Borevitz JO, Li WH, Shiu SH (2007) A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res 17:632-640.
14. DeBlasio SL, Leusse DL, Hangarter RP (2005) A plant-specific protein essential for blue-light-induced chloroplast movements. Plant Physiol 139:101-114.
15. Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4:10.
16. Wang B, Brendel V (2006) Genomewide comparative analysis of alternative splicing in plants. PNAS 103:7175-7180.