CYGD: The Comprehensive Yeast Genome Database

Nucleic Acids Research

Volumn 33, Issue DATABASE ISS., 2005, Pages

  Guldener U ^a   Munsterkotter M ^a   Kastenmuller G ^a   Strack, N ^j   van Helden, J ^b   Lemer, C ^b   Richelles, J ^b   Wodak, S J ^b   Garcia Martinez J ^c   Perez Ortin J E ^c   Michael, H ^d   Kaps, A ^e   Talla, E ^f   Dujon, B ^g   Andre B ^b   Souciet, J L ^h   De Montigny, J ^h   Bon, E ^i,k   Gaillardin, C ⁱ   Mewes, H W ^a,j  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^c UNIVERSITY OF VALENCIA   (Spain)

^d UNIVERSITY OF GÖTTINGEN   (Germany)

^e Biomax Informatics AG   (Germany)

^f AIX MARSEILLE UNIVERSITÉ   (France)

^g SORBONNE UNIVERSITÉ   (France)

^h UNIVERSITÉ DE STRASBOURG   (France)

ⁱ CNRS   (France)

^j TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^k UNIVERSITÉ DE BORDEAUX   (France)

more..

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; TRANSCRIPTION FACTOR;

ACCESS TO INFORMATION; ARTICLE; CELL COMMUNICATION; CELL FUNCTION; CELL TRANSPORT; COMPREHENSIVE YEAST GENOME DATABASE; DNA RESPONSIVE ELEMENT; EUKARYOTE; EUROPE; FUNGAL METABOLISM; GENE CLUSTER; GENE CONTROL; GENE FUNCTION; GENE SEQUENCE; GENETIC DATABASE; GENETIC MODEL; GENOME ANALYSIS; INFORMATION PROCESSING; INTERNET; MEDICAL INFORMATION SYSTEM; MOLECULAR PHYLOGENY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN INTERACTION; PUBLICATION; REGULATORY MECHANISM; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; SIMILARITY MATRIX OF PROTEINS; YEAST CELL; BINDING SITE; CLUSTER ANALYSIS; CONTROLLED STUDY; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; REFERENCE DATABASE; SEQUENCE ANALYSIS; SPECIES DIFFERENCE;

BINDING SITES; DATABASES, GENETIC; GENOME, FUNGAL; GENOMICS; MEMBRANE PROTEINS; MEMBRANE TRANSPORT PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ANALYSIS, PROTEIN; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 13444306676     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki053     Document Type: Article

References (30)

1. Mewes,H.W., Albermann,K., Bahr,M., Frishman,D., Gleissner,A., Hani,J., Heumann,K., Kleine,K., Maierl,A., Oliver,S.G. et al. (1997) Overview of the yeast genome. Nature, 387, 7-8.
2. Dujon,B. (1998) European Functional Analysis Network (EUROFAN) and the functional analysis of the Saccharomyces cerevisiae genome. Electrophoresis, 19, 617-624.
3. Souciet,J.L., Aigle,M., Artiguenave,F., Blandin,G., Bolotin-Fukuhara,M., Bon,E., Brottier,P., Casaregola,S., de Montigny,J., Dujon,B. et al. (2000) Genomic exploration of the Hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett., 487, 3-12.
4. Kellis,M., Patterson,N., Endrizzi,M., Birren,B. and Lander,E.S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254.
5. Cliften,P., Sudarsanam,P., Desikan,A., Fulton,L., Fulton,B., Majors,J., Waterston,R., Cohen,B.A. and Johnston,M. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science, 301, 71-76.
6. Winzeler,E.A., Shoemaker,D.D., Astromoff,A., Liang,H., Anderson,K., Andre,B., Bangham,R., Benito,R., Boeke,J.D., Bussey,H. et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science, 285, 901-906.
7. Giaever,G., Chu,A.M., Ni,L., Connelly,C., Riles,L., Veronneau,S., Dow,S., Lucau-Danila,A., Anderson,K., Andre,B. et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418, 387-391.
8. Christie,K.R., Weng,S., Balakrishnan,R., Costanzo,M.C., Dolinski,K., Dwight,S.S., Engel,S.R., Feierbach,B., Fisk,D.G., Hirschman,J.E. et al. (2004) Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res., 32 (Database issue), D311-D314.
9. Bon,E., Casaregola,S., Blandin,G., Llorente,B., Neuveglise,C., Münsterkotter,M., Güldener,U., Mewes,H.W., van Helden,J., Dujon,B. et al. (2003) Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns. Nucleic Acids Res., 31, 1121-1135.
10. van Helden,J., del Olmo,M. and Perez-Ortin,J.E. (2000) Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res., 28, 1000-1010.
11. Gross,S. and Moore,C.L. (2001) Rna15 interaction with the A-rich yeast polyadenylation signal is an essential step in mRNA 3′ -end formation. Mol. Cell. Biol., 21, 8045-8055.
12. Dichtl,B. and Keller,W. (2001) Recognition of polyadenylation sites in yeast pre-mRNAs by cleavage and polyadenylation factor. EMBO J., 20, 3197-3209.
13. Clarke,L. (1998) Centromeres: proteins, protein complexes, and repeated domains at centromeres of simple eukaryotes. Curr. Opin. Genet. Dev., 8, 212-218.
14. Van Belle,D. and Andre,B. (2001) A genomic view of yeast membrane transporters. Curr. Opin. Cell Biol., 13, 389-398.
15. De Hertogh,B., Carvajal,E., Talla,E., Dujon,B., Baret,P. and Goffeau,A. (2002) Phylogenetic classification of transporters and other membrane proteins from Saccharomyces cerevisiae. Funct. Integr. Genomics, 2, 154-170.
16. Matys,V., Fricke,E., Geffers,R., Gossling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas,D., Kel,A.E., Kel-Margoulis,O.V. et al. (2003) TRANSFAC®: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
17. Simonis,N., Wodak,S.J., Cohen,G.N. and van Helden,J. (2004) Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinformatics, 20, 2370-2379.
18. Lemer,C., Antezana,E., Couche,F., Fays,F., Santolaria,X., Janky,R., Deville,Y., Richelle,J. and Wodak,S.J. (2004) The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Res., 32 (Database issue), D443-D448.
19. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene Ontology: tool for the unification of biology. Nature Genet., 25, 25-29.
20. Kanehisa,M., Goto,S., Kawashima,S., Okuno,Y. and Hattori,M. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res., 32 (Database issue), D277-D280.
21. Michal,G. (1998) Biochemical Pathways: An Altlas of Biochemistry and Molecular Biology. Wiley and Sons, Inc.
22. Hermjakob,H., Montecchi-Palazzi,L., Bader,G., Wojcik,R., Salwinski,L., Ceol,A., Moore,S., Orchard,S., Sarkans,U., von Mering,C. et al. (2004) The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nat. Biotechnol., 22, 177-183.
23. Strack,N. and Mewes,H.W. (1999) SESAM: Seed Extraction Sequence Analysis Method. Proc. GCB, 1, 59-65.
24. Wood,V., Gwilliam,R., Rajandream,M.A., Lyne,M., Lyne,R., Stewart,A., Sgouros,J., Peat,N., Hayles,J., Baker,S. et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature, 415 871-880.
25. Dujon,B., Sherman,D., Fischer,G., Durrens,P., Casaregola,S., Lafontaine,I., de Montigny,J., Marck,C., Neuveglise,C., Talla,E. et al. (2004) Genome evolution in yeasts. Nature, 430, 35-44.
26. Frishman,D., Mokrejs,M., Kosykh,D., Kastenmuller,G., Kolesov,G., Zubrzycki,I., Gruber,C., Geier,B., Kaps,A., Albermann,K. et al. (2003) The PEDANT genome database. Nucleic Acids Res., 31, 207-211.
27. Talla,E., Tekaia,F., Brino,L. and Dujon,B. (2003) A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization. BMC Genomics, 4, 38.
28. Kellis,M., Birren,B.W. and Lander,E.S. (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature, 428, 617-624.
29. Dietrich,F.S., Voegeli,S., Brachat,S., Lerch,A., Gates,K., Steiner,S., Mohr,C., Pohlmann,R., Luedi,P., Choi,S.D. et al. (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science, 304, 304-307.
30. Pearson,W.R. (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol., 132, 185-219.