Gene Ontology annotations at SGD: New data sources and annotation methods

Nucleic Acids Research

Volumn 36, Issue SUPPL. 1, 2008, Pages

  Hong, Eurie L ^a   Balakrishnan, Rama ^a   Dong, Qing ^a   Christie, Karen R ^a   Park, Julie ^a   Binkley, Gail ^a   Costanzo, Maria C ^a   Dwight, Selina S ^a   Engel, Stacia R ^a   Fisk, Dianna G ^a   Hirschman, Jodi E ^a   Hitz, Benjamin C ^a   Krieger, Cynthia J ^a   Livstone, Michael S ^b   Miyasato, Stuart R ^a   Nash, Robert S ^a   Oughtred, Rose ^b   Skrzypek, Marek S ^a   Weng, Shuai ^a   Wong, Edith D ^a   Zhu, Kathy K ^a   Dolinski, Kara ^b   Botstein, David ^b   Cherry, J Michael ^a   more..

^a STANFORD UNIVERSITY   (United States)

^b PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT;

ARTICLE; COMPUTER INTERFACE; DATA ANALYSIS; FUNGAL GENE; GENETIC ANALYSIS; GENETIC DATABASE; GENOMICS; HIGH THROUGHPUT SCREENING; INFORMATION PROCESSING; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES GENOME DATABASE;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENES, FUNGAL; GENOME, FUNGAL; GENOMICS; INTERNET; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; USER-COMPUTER INTERFACE; VOCABULARY, CONTROLLED;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

EID: 38549123363     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm909     Document Type: Article

References (17)

1. Gene Ontology Consortium, (2006) The Gene Ontology (GO) project in 2006. Nucleic Acids Res., 34, 326.
2. Dwight, S.S., Dolinski, K., Ball, C.A., Binkley, G., Christie, K.R., Fisk, D.G., Issel-Tarver, L., Schroeder, M. et al. (2002) Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res., 30, 69-72.
3. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
4. Gene Ontology Consortium, (2001) Creating the gene ontology resource: design and implementation. Genome Res., 11, 1425-1433.
5. Dolinski, K. (2005) Changing perspectives in yeast research nearly a decade after the genome sequence. Genome Res., 15, 1611-1619.
6. Pena-Gastillo, L. and Hughes, T.R. (2007) Why are there still over 1000 uncharacterized yeast genes? Genetics, 176, 7-14.
7. Huh, W.K., Falvo, J.V., Gerke, L.C., Carroll, A.S., Howson, R.W., Weissman, J.S. and O'Shea, E.K. (2003) Global analysis of protein localization in budding yeast. Nature, 425, 686-691.
8. Kumar, A., Agarwal, S., Heyman, J.A., Matson, S., Heidtman, M., Piccirillo, S., Umansky, L., Drawid, A., Jansen, R. et al. (2002) Subcellular localization of the yeast proteome. Gen. Dev., 16 707-719.
9. Hirschman, J.E., Balakrishnan, R., Christie, K.R., Costanzo, M.C., Dwight, S.S., Engel, S.R., Fisk, D.G., Hong, E.L., Livstone, M.S. et al. (2006) Genome Snapshot: A new resource at the Saccharomyces Gcnome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res., 34, D442-D445.
10. Camon, E., Magrane, M., Barrell, D., Lee, V., Dimmer, E., Maslen, J., Binns, D., Harte, N., Lopez, R. et al. (2004) The Gene Ontology Annotation (GOA) Database: Sharing knowledge in UniProt with Gene Ontology. Nucleic Acids Res., 32, D262-D266.
11. Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R. and Lopez, R. (2005) InterProScan: Protein domains identifier. Nucleic Acids Res., 33, W116-W120.
12. Hanna, J.S., Kroll, E.S., Lundblad, V. and Spencer, F.A. (2001) Saccharomyces cerevisiae CTF18 and CTF4 are required for sister chromatid cohesion. Mol. Cell. Biol., 21, 3144-3158.
13. Mayer, M.L., Gygi, S.P., Aebersold, R. and Hieter, P. (2001) Identification of RFC(Ctf18p, Ctf8p, Dcc1p): An alternative RFC complex required for sister chromatid cohesion in S. cerevisiae. Mol. Cell 7, 959-970.
14. Jansen, R., Yu, H., Greenbaum, D., Kluger, Y., Krogan, N.J., Chung, S., Emili, A., Snyder, M., Greenblatt, J.F. et al. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science, 302, 449-453.
15. Lee, I., Date, S.V., Adai, A.T. and Marcotte, E.M. (2004) A probabilistic functional network of yeast genes. Science, 306 1555-1558.
16. Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P. et al. (2005) InterPro, progress and status in 2005. Nucleic Acids Res., 33 D201-D205.
17. Troyanskaya, O.G., Dolinski, K., Owen, A.B., Altman, R.B. and Botstein, D. (2003) A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc. Natl Acad. Sci. USA, 100, 8348-8353.