Literature DB >> 10592186

Integrating functional genomic information into the Saccharomyces genome database.

C A Ball1, 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.   

Abstract

The Saccharomyces Genome Database (SGD) stores and organizes information about the nearly 6200 genes in the yeast genome. The information is organized around the 'locus page' and directs users to the detailed information they seek. SGD is endeavoring to integrate the existing information about yeast genes with the large volume of data generated by functional analyses that are beginning to appear in the literature and on web sites. New features will include searches of systematic analyses and Gene Summary Paragraphs that succinctly review the literature for each gene. In addition to current information, such as gene product and phenotype descriptions, the new locus page will also describe a gene product's cellular process, function and localization using a controlled vocabulary developed in collaboration with two other model organism databases. We describe these developments in SGD through the newly reorganized locus page. The SGD is accessible via the WWW at http://genome-www.stanford.edu/Saccharomyces/

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Year:  2000        PMID: 10592186      PMCID: PMC102447          DOI: 10.1093/nar/28.1.77

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


  15 in total

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Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

2.  MIPS: a database for genomes and protein sequences.

Authors:  H W Mewes; K Heumann; A Kaps; K Mayer; F Pfeiffer; S Stocker; D Frishman
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

3.  The FlyBase database of the Drosophila Genome Projects and community literature.

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Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

4.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999.

Authors:  A Bairoch; R Apweiler
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

5.  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

6.  Genetic and physical maps of Saccharomyces cerevisiae.

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7.  The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data.

Authors:  P E Hodges; A H McKee; B P Davis; W E Payne; J I Garrels
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

8.  Cluster analysis and display of genome-wide expression patterns.

Authors:  M B Eisen; P T Spellman; P O Brown; D Botstein
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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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  33 in total

1.  The Stanford Microarray Database.

Authors:  G Sherlock; T Hernandez-Boussard; A Kasarskis; G Binkley; J C Matese; S S Dwight; M Kaloper; S Weng; H Jin; C A Ball; M B Eisen; P T Spellman; P O Brown; D Botstein; J M Cherry
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.

Authors:  J Qian; B Stenger; C A Wilson; J Lin; R Jansen; S A Teichmann; J Park; W G Krebs; H Yu; V Alexandrov; N Echols; M Gerstein
Journal:  Nucleic Acids Res       Date:  2001-04-15       Impact factor: 16.971

3.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

4.  Creating the gene ontology resource: design and implementation.

Authors: 
Journal:  Genome Res       Date:  2001-08       Impact factor: 9.043

5.  PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches.

Authors:  W Fujibuchi; J S Anderson; D Landsman
Journal:  Nucleic Acids Res       Date:  2001-10-01       Impact factor: 16.971

6.  cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships.

Authors:  K Birnbaum; P N Benfey; D E Shasha
Journal:  Genome Res       Date:  2001-09       Impact factor: 9.043

7.  Changes in global gene expression patterns during development and maturation of the rat kidney.

Authors:  R O Stuart; K T Bush; S K Nigam
Journal:  Proc Natl Acad Sci U S A       Date:  2001-05-01       Impact factor: 11.205

8.  Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes.

Authors:  S A Jelinsky; P Estep; G M Church; L D Samson
Journal:  Mol Cell Biol       Date:  2000-11       Impact factor: 4.272

9.  Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases.

Authors:  Charles Brenner
Journal:  Biochemistry       Date:  2002-07-23       Impact factor: 3.162

10.  Responses of pathogenic and nonpathogenic yeast species to steroids reveal the functioning and evolution of multidrug resistance transcriptional networks.

Authors:  Dibyendu Banerjee; Gaelle Lelandais; Sudhanshu Shukla; Gauranga Mukhopadhyay; Claude Jacq; Frederic Devaux; Rajendra Prasad
Journal:  Eukaryot Cell       Date:  2007-11-09
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