GO-module: Functional synthesis and improved interpretation of gene ontology patterns

Bioinformatics

Volumn 27, Issue 10, 2011, Pages 1444-1446

  Yang, Xinan ^a   Li, Jianrong ^a   Lee, Younghee ^a   Lussier, Yves A ^a,b  

^a Center for Biomedical Informatics   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE; INTERNET; LINGUISTICS; NOMENCLATURE;

GENES; INTERNET; SOFTWARE; TERMINOLOGY AS TOPIC; USER-COMPUTER INTERFACE; VOCABULARY, CONTROLLED;

EID: 79955771442     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr142     Document Type: Article

References (24)

1. Alterovitz, G. et al. (2007) GO PaD: the Gene Ontology partition database. Nucleic Acids Res., 35, D322-D327.
2. Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
3. Atanur, S.S. et al. (2010) The genome sequence of the spontaneously hypertensive rat: analysis and functional significance. Genome Res., 20, 791-803.
4. Burke, M.K. et al. (2010) Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature, 467, 587-590.
5. Cho, Y.R. et al. (2007) Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics, 8, 265.
6. Dennis, G. Jr et al. (2003) DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol., 4, P3.
7. Draghici, S. et al. (2003a) Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res., 31, 3775-3781.
8. Draghici, S. et al. (2003b) Global functional profiling of gene expression. Genomics, 81, 98-104.
9. Falcon, S. and Gentleman, R. (2007) Using GOstats to test gene lists for GO term association. Bioinformatics, 23, 257-258.
10. Grossmann, S. et al. (2007) Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. Bioinformatics, 23, 3024-3031.
11. Harris, M.A. et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res., 32, D258-D261.
12. Heinig, M. et al. (2010) A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature, 467, 460-464.
13. Hoffman, M.M. and Birney, E. (2010) An effective model for natural selection in promoters. Genome Res., 20, 685-692.
14. Lee, Y. et al. (2010) Network modeling identifies molecular functions targeted by mir-204 to suppress head and neck tumor metastasis. PLoS Comput. Biol., 6, e1000730.
15. Liu, G.E. et al. (2010) Analysis of copy number variations among diverse cattle breeds. Genome Res., 20, 693-703.
16. Marcucci, G. et al. (2008) MicroRNA expression in cytogenetically normal acute myeloid leukemia. N. Engl. J. Med., 358, 1919-1928.
17. Mortazavi, A. et al. (2010) Scaffolding a Caenorhabditis nematode genome with RNAseq. Genome Res., 20, 1740-1747.
18. Rhee, S.Y. et al. (2008) Use and misuse of the gene ontology annotations. Nat. Rev. Genet., 9, 509-515.
19. Smukalla, S. et al. (2008) FLO1 is a variable green beard gene that drives biofilm-like cooperation in budding yeast. Cell, 135, 726-737.
20. Somel, M. et al. (2010) MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. Genome Res., 20, 1207-1218.
21. Swanson-Wagner, R.A. et al. (2010) Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res., 20, 1689-1699.
22. Vinuela, A. et al. (2010) Genome-wide gene expression regulation as a function of genotype and age in C.elegans. Genome Res., 20, 929-937.
23. Wolfe, C.J. et al. (2005) Systematic survey reveals general applicability of "guilt-byassociation" within gene coexpression networks. BMC Bioinformatics, 6, 227.
24. Yamaguchi, K. et al. (2010) Identification of an ovarian clear cell carcinoma gene signature that reflects inherent disease biology and the carcinogenic processes. Oncogene, 29, 1741-1752.