Saccharomyces Genome Database Provides Tools to Survey Gene Expression and Functional Analysis Data

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2000 Jan 11

PMID 11125055

Citations 32

Authors

C A Ball

H Jin

G Sherlock

S Weng

J C Matese

R Andrada

G Binkley

K Dolinski

S S Dwight

M A Harris

M Schroeder

D Botstein

J M Cherry

Affiliations

Soon will be listed here.

Abstract

Upon the completion of the SACCHAROMYCES: cerevisiae genomic sequence in 1996 [Goffeau,A. et al. (1997) NATURE:, 387, 5], several creative and ambitious projects have been initiated to explore the functions of gene products or gene expression on a genome-wide scale. To help researchers take advantage of these projects, the SACCHAROMYCES: Genome Database (SGD) has created two new tools, Function Junction and Expression Connection. Together, the tools form a central resource for querying multiple large-scale analysis projects for data about individual genes. Function Junction provides information from diverse projects that shed light on the role a gene product plays in the cell, while Expression Connection delivers information produced by the ever-increasing number of microarray projects. WWW access to SGD is available at genome-www.stanford. edu/Saccharomyces/.

Citing Articles

New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources.

Engel S, Wong E, Nash R, Aleksander S, Alexander M, Douglass E Genetics. 2021; 220(4).

PMID: 34897464 PMC: 9209811. DOI: 10.1093/genetics/iyab224.

Yeast as a Model to Understand Actin-Mediated Cellular Functions in Mammals-Illustrated with Four Actin Cytoskeleton Proteins.

Akram Z, Ahmed I, Mack H, Kaur R, Silva R, Castilho B Cells. 2020; 9(3).

PMID: 32164332 PMC: 7140605. DOI: 10.3390/cells9030672.

Cross-stress resistance in Saccharomyces cerevisiae yeast--new insight into an old phenomenon.

Swiecilo A Cell Stress Chaperones. 2016; 21(2):187-200.

PMID: 26825800 PMC: 4786536. DOI: 10.1007/s12192-016-0667-7.

Copy-number variation of cancer-gene orthologs is sufficient to induce cancer-like symptoms in Saccharomyces cerevisiae.

de Clare M, Oliver S BMC Biol. 2013; 11:24.

PMID: 23531409 PMC: 3635878. DOI: 10.1186/1741-7007-11-24.

Comparative gene expression between two yeast species.

Guan Y, Dunham M, Troyanskaya O, Caudy A BMC Genomics. 2013; 14:33.

PMID: 23324262 PMC: 3556494. DOI: 10.1186/1471-2164-14-33.

References

Chervitz S, Hester E, Ball C, Dolinski K, Dwight S, Harris M . Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Nucleic Acids Res. 1998; 27(1):74-8. PMC: 148101. DOI: 10.1093/nar/27.1.74. View

Spellman P, Sherlock G, Zhang M, Iyer V, Anders K, Eisen M . Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 1998; 9(12):3273-97. PMC: 25624. DOI: 10.1091/mbc.9.12.3273. View

Pellegrini M, Marcotte E, Thompson M, Eisenberg D, Yeates T . Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A. 1999; 96(8):4285-8. PMC: 16324. DOI: 10.1073/pnas.96.8.4285. View

Marcotte E, Pellegrini M, Ng H, Rice D, Yeates T, Eisenberg D . Detecting protein function and protein-protein interactions from genome sequences. Science. 1999; 285(5428):751-3. DOI: 10.1126/science.285.5428.751. View

Ferea T, Botstein D, Brown P, Rosenzweig R . Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci U S A. 1999; 96(17):9721-6. PMC: 22277. DOI: 10.1073/pnas.96.17.9721. View

Marcotte E, Pellegrini M, Thompson M, Yeates T, Eisenberg D . A combined algorithm for genome-wide prediction of protein function. Nature. 1999; 402(6757):83-6. DOI: 10.1038/47048. View

Ross-Macdonald P, Coelho P, Roemer T, Agarwal S, Kumar A, Jansen R . Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature. 1999; 402(6760):413-8. DOI: 10.1038/46558. View

Wyrick J, Holstege F, Jennings E, Causton H, Shore D, Grunstein M . Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature. 1999; 402(6760):418-21. DOI: 10.1038/46567. View

Ball C, Dolinski K, Dwight S, Harris M, Kasarskis A, Scafe C . Integrating functional genomic information into the Saccharomyces genome database. Nucleic Acids Res. 1999; 28(1):77-80. PMC: 102447. DOI: 10.1093/nar/28.1.77. View

10.

Roberts C, Nelson B, Marton M, STOUGHTON R, Meyer M, Bennett H . Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science. 2000; 287(5454):873-80. DOI: 10.1126/science.287.5454.873. View

11.

Uetz P, Giot L, Cagney G, Mansfield T, Judson R, Knight J . A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 2000; 403(6770):623-7. DOI: 10.1038/35001009. View

12.

Velculescu V, Zhang L, Zhou W, Vogelstein J, Basrai M, Bassett Jr D . Characterization of the yeast transcriptome. Cell. 1997; 88(2):243-51. DOI: 10.1016/s0092-8674(00)81845-0. View

13.

DeRisi J, Iyer V, Brown P . Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 1997; 278(5338):680-6. DOI: 10.1126/science.278.5338.680. View

14.

Cherry J, Adler C, Ball C, Chervitz S, Dwight S, Hester E . SGD: Saccharomyces Genome Database. Nucleic Acids Res. 1998; 26(1):73-9. PMC: 147204. DOI: 10.1093/nar/26.1.73. View

15.

Cho R, Campbell M, Winzeler E, Steinmetz L, Conway A, Wodicka L . A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell. 1998; 2(1):65-73. DOI: 10.1016/s1097-2765(00)80114-8. View

16.

Chu S, Derisi J, Eisen M, Mulholland J, Botstein D, Brown P . The transcriptional program of sporulation in budding yeast. Science. 1998; 282(5389):699-705. DOI: 10.1126/science.282.5389.699. View

17.

Holstege F, Jennings E, Wyrick J, Lee T, Hengartner C, Green M . Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998; 95(5):717-28. DOI: 10.1016/s0092-8674(00)81641-4. View

18.

Chervitz S, Aravind L, Sherlock G, Ball C, Koonin E, Dwight S . Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science. 1998; 282(5396):2022-8. PMC: 3057080. DOI: 10.1126/science.282.5396.2022. View