Literature DB >> 11125055

Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data.

C A Ball1, H Jin, G Sherlock, S Weng, J C Matese, R Andrada, G Binkley, K Dolinski, S S Dwight, M A Harris, L Issel-Tarver, M Schroeder, D Botstein, J M Cherry.   

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/.

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Year:  2001        PMID: 11125055      PMCID: PMC29796          DOI: 10.1093/nar/29.1.80

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  18 in total

1.  Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast.

Authors:  J J Wyrick; F C Holstege; E G Jennings; H C Causton; D Shore; M Grunstein; E S Lander; R A Young
Journal:  Nature       Date:  1999-11-25       Impact factor: 49.962

2.  Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles.

Authors:  C J Roberts; B Nelson; M J Marton; R Stoughton; M R Meyer; H A Bennett; Y D He; H Dai; W L Walker; T R Hughes; M Tyers; C Boone; S H Friend
Journal:  Science       Date:  2000-02-04       Impact factor: 47.728

3.  Detecting protein function and protein-protein interactions from genome sequences.

Authors:  E M Marcotte; M Pellegrini; H L Ng; D W Rice; T O Yeates; D Eisenberg
Journal:  Science       Date:  1999-07-30       Impact factor: 47.728

4.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.

Authors:  M Pellegrini; E M Marcotte; M J Thompson; D Eisenberg; T O Yeates
Journal:  Proc Natl Acad Sci U S A       Date:  1999-04-13       Impact factor: 11.205

5.  Integrating functional genomic information into the Saccharomyces genome database.

Authors:  C A Ball; K Dolinski; S S Dwight; M A Harris; L Issel-Tarver; A Kasarskis; C R Scafe; G Sherlock; G Binkley; H Jin; M Kaloper; S D Orr; M Schroeder; S Weng; Y Zhu; D Botstein; J M Cherry
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

6.  A combined algorithm for genome-wide prediction of protein function.

Authors:  E M Marcotte; M Pellegrini; M J Thompson; T O Yeates; D Eisenberg
Journal:  Nature       Date:  1999-11-04       Impact factor: 49.962

7.  Large-scale analysis of the yeast genome by transposon tagging and gene disruption.

Authors:  P Ross-Macdonald; P S Coelho; T Roemer; S Agarwal; A Kumar; R Jansen; K H Cheung; A Sheehan; D Symoniatis; L Umansky; M Heidtman; F K Nelson; H Iwasaki; K Hager; M Gerstein; P Miller; G S Roeder; M Snyder
Journal:  Nature       Date:  1999-11-25       Impact factor: 49.962

8.  Systematic changes in gene expression patterns following adaptive evolution in yeast.

Authors:  T L Ferea; D Botstein; P O Brown; R F Rosenzweig
Journal:  Proc Natl Acad Sci U S A       Date:  1999-08-17       Impact factor: 11.205

9.  Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure.

Authors:  S A Chervitz; E T Hester; C A Ball; K Dolinski; S S Dwight; M A Harris; G Juvik; A Malekian; S Roberts; T Roe; C Scafe; M Schroeder; G Sherlock; S Weng; Y Zhu; J M Cherry; D Botstein
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

10.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.

Authors:  P T Spellman; G Sherlock; M Q Zhang; V R Iyer; K Anders; M B Eisen; P O Brown; D Botstein; B Futcher
Journal:  Mol Biol Cell       Date:  1998-12       Impact factor: 4.138

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  27 in total

1.  yMGV: helping biologists with yeast microarray data mining.

Authors:  Stéphane Le Crom; Frédéric Devaux; Claude Jacq; Philippe Marc
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

2.  yMGV: a database for visualization and data mining of published genome-wide yeast expression data.

Authors:  P Marc; F Devaux; C Jacq
Journal:  Nucleic Acids Res       Date:  2001-07-01       Impact factor: 16.971

3.  Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks.

Authors:  Paul Grosu; Jeffrey P Townsend; Daniel L Hartl; Duccio Cavalieri
Journal:  Genome Res       Date:  2002-07       Impact factor: 9.043

4.  Arabidopsis MPSS. An online resource for quantitative expression analysis.

Authors:  Blake C Meyers; David K Lee; Tam H Vu; Shivakundan Singh Tej; Steve B Edberg; Marta Matvienko; Larry D Tindell
Journal:  Plant Physiol       Date:  2004-06-01       Impact factor: 8.340

5.  The use of MPSS for whole-genome transcriptional analysis in Arabidopsis.

Authors:  Blake C Meyers; Shivakundan Singh Tej; Tam H Vu; Christian D Haudenschild; Vikas Agrawal; Steve B Edberg; Hassan Ghazal; Shannon Decola
Journal:  Genome Res       Date:  2004-08       Impact factor: 9.043

6.  Yeast genomics: past, present, and future promise.

Authors:  Michael Snyder; Anuj Kumar
Journal:  Funct Integr Genomics       Date:  2002-09       Impact factor: 3.410

7.  The TRIPLES database: a community resource for yeast molecular biology.

Authors:  Anuj Kumar; Kei-Hoi Cheung; Nick Tosches; Peter Masiar; Yang Liu; Perry Miller; Michael Snyder
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

8.  Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).

Authors:  Selina S Dwight; Midori A Harris; Kara Dolinski; Catherine A Ball; Gail Binkley; Karen R Christie; Dianna G Fisk; Laurie Issel-Tarver; Mark Schroeder; Gavin Sherlock; Anand Sethuraman; Shuai Weng; David Botstein; J Michael Cherry
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

9.  SCMD: Saccharomyces cerevisiae Morphological Database.

Authors:  Taro L Saito; Miwaka Ohtani; Hiroshi Sawai; Fumi Sano; Ayaka Saka; Daisuke Watanabe; Masashi Yukawa; Yoshikazu Ohya; Shinichi Morishita
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

10.  From gene networks to gene function.

Authors:  Thomas Schlitt; Kimmo Palin; Johan Rung; Sabine Dietmann; Michael Lappe; Esko Ukkonen; Alvis Brazma
Journal:  Genome Res       Date:  2003-12       Impact factor: 9.043

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