CYGD: the Comprehensive Yeast Genome Database

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2004 Dec 21

PMID 15608217

Citations 130

Authors

U Guldener

M Munsterkotter

G Kastenmuller

N Strack

J van Helden

C Lemer

J Richelles

S J Wodak

J Garcia-Martinez

J E Perez-Ortin

H Michael

A Kaps

E Talla

B Dujon

B Andre

J L Souciet

J De Montigny

E Bon

C Gaillardin

H W Mewes

Affiliations

Soon will be listed here.

Abstract

The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the best understood model organism for eukaryotes. The database serves as a common resource generated by a European consortium, going beyond the provision of sequence information and functional annotations on individual genes and proteins. In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements. These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters. As more yeast genomes are published, their annotation becomes greatly facilitated using S.cerevisiae as a reference. CYGD provides a way of exploring related genomes with the aid of the S.cerevisiae genome as a backbone and SIMAP, the Similarity Matrix of Proteins. The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.

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References

Pearson W . Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol. 1999; 132:185-219. DOI: 10.1385/1-59259-192-2:185. View

Winzeler E, Shoemaker D, Astromoff A, Liang H, Anderson K, Andre B . Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 1999; 285(5429):901-6. DOI: 10.1126/science.285.5429.901. View

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

Souciet J, Aigle M, Artiguenave F, Blandin G, Bolotin-Fukuhara M, Bon E . Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett. 2001; 487(1):3-12. DOI: 10.1016/s0014-5793(00)02272-9. View

Dichtl B, Keller W . Recognition of polyadenylation sites in yeast pre-mRNAs by cleavage and polyadenylation factor. EMBO J. 2001; 20(12):3197-209. PMC: 150212. DOI: 10.1093/emboj/20.12.3197. View

Van Belle D, Andre B . A genomic view of yeast membrane transporters. Curr Opin Cell Biol. 2001; 13(4):389-98. DOI: 10.1016/s0955-0674(00)00226-x. View

Gross S, Moore C . Rna15 interaction with the A-rich yeast polyadenylation signal is an essential step in mRNA 3'-end formation. Mol Cell Biol. 2001; 21(23):8045-55. PMC: 99971. DOI: 10.1128/MCB.21.23.8045-8055.2001. View

Wood V, Gwilliam R, Rajandream M, LYNE M, Lyne R, Stewart A . The genome sequence of Schizosaccharomyces pombe. Nature. 2002; 415(6874):871-80. DOI: 10.1038/nature724. View

Giaever G, Chu A, Ni L, Connelly C, Riles L, Veronneau S . Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002; 418(6896):387-91. DOI: 10.1038/nature00935. View

10.

De Hertogh B, Carvajal E, Talla E, Dujon B, Baret P, Goffeau A . Phylogenetic classification of transporters and other membrane proteins from Saccharomyces cerevisiae. Funct Integr Genomics. 2002; 2(4-5):154-70. DOI: 10.1007/s10142-002-0060-8. View

11.

Frishman D, Mokrejs M, Kosykh D, Kastenmuller G, Kolesov G, Zubrzycki I . The PEDANT genome database. Nucleic Acids Res. 2003; 31(1):207-11. PMC: 165452. DOI: 10.1093/nar/gkg005. View

12.

Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R . TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 2003; 31(1):374-8. PMC: 165555. DOI: 10.1093/nar/gkg108. View

13.

Bon E, Casaregola S, Blandin G, Llorente B, Neuveglise C, Munsterkotter M . Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns. Nucleic Acids Res. 2003; 31(4):1121-35. PMC: 150231. DOI: 10.1093/nar/gkg213. View

14.

Kellis M, Patterson N, Endrizzi M, Birren B, Lander E . Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003; 423(6937):241-54. DOI: 10.1038/nature01644. View

15.

Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J . Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science. 2003; 301(5629):71-6. DOI: 10.1126/science.1084337. View

16.

Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M . The KEGG resource for deciphering the genome. Nucleic Acids Res. 2003; 32(Database issue):D277-80. PMC: 308797. DOI: 10.1093/nar/gkh063. View

17.

Christie K, Weng S, Balakrishnan R, Costanzo M, Dolinski K, Dwight S . Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2003; 32(Database issue):D311-4. PMC: 308767. DOI: 10.1093/nar/gkh033. View

18.

Lemer C, Antezana E, Couche F, Fays F, Santolaria X, Janky R . The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Res. 2003; 32(Database issue):D443-8. PMC: 308873. DOI: 10.1093/nar/gkh139. View

19.

Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A . The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol. 2004; 22(2):177-83. DOI: 10.1038/nbt926. View

20.

Kellis M, Birren B, Lander E . Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004; 428(6983):617-24. DOI: 10.1038/nature02424. View