Genomics confounds gene classification

American Scientist

Volumn 96, Issue 6, 2008, Pages 466-473

  Seringhaus, Michael ^a   Gerstein, Mark ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME; CLASSIFICATION; GENE; GENETICS; GENOMICS; MOLECULAR ANALYSIS; MUTATION; NOMENCLATURE; PROTEIN;

EID: 77951583413     PISSN: 00030996     EISSN: None     Source Type: Trade Journal    
DOI: 10.1511/2008.75.466     Document Type: Article

References (13)

1. The ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1 percent of the human genome by the ENCODE pilot project. Nature 447: 799-816.
2. Gerstein, M. B., et al. 2007. What is a gene, post-ENCODE? History and updated definition. Genome Research 17: 669-681.
3. Seringhaus, M. R., P. D. Cayting and M. B. Gerstein. 2008. Uncovering trends in gene naming. Genome Biology 9: 401.
4. Kapranov, P., et al. 2007. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316: 1484-1488.
5. Kapranov, P., A. T. Willingham and T. R. Gingeras. 2007. Genome-wide transcription and the implications for genomic organization. Nature Review Genetics. 8: 413-423.
6. The Gene Ontology Consortium. 2008. The Gene Ontology project in 2008. Nucleic Acids Research 36: 440-444.
7. Lu, L. J., et al. 2007; Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends in Biochemical Science 32: 320-331.
8. Berners-Lee, T., J. Hendler and O. Lassila. 2001. The Semantic Web: A new form of Web content that is meaningful to computers will unleash a revolution of new possibilities. Scientific American 284: 29-37.
9. Finn, R. D., et al. 2008. The Pfam protein families database. Nucleic Acids Research 36: 281-288.
10. Mewes, H. W., et al. 2008. MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Research. 36: 196-201.
11. UniProt Consortium. 2007. The universal protein resource (UniProt). Nucleic Acids Research 36: 190-195.
12. Wu, J. Q., et al. 2008. Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biology 9: R3.
13. Zheng, D., and M. B. Gerstein. 2007. The ambiguous boundary between genes and pseudogenes: The dead rise up, or do they? Trends in Genetics 23: 219-224.