Literature DB >> 14681424

yMGV: a cross-species expression data mining tool.

Gaëlle Lelandais1, Stéphane Le Crom, Frédéric Devaux, Stéphane Vialette, George M Church, Claude Jacq, Philippe Marc.   

Abstract

The yeast Microarray Global Viewer (yMGV @ http://transcriptome.ens.fr/ymgv) was created 3 years ago as a database that houses a collection of Saccharomyces cerevisiae and Schizosaccharo myces pombe microarray data sets published in 82 different articles. yMGV couples data mining tools with a user-friendly web interface so that, with a few mouse clicks, one can identify the conditions that affect the expression of a gene or list of genes regulated in a set of experiments. One of the major new features we present here is a set of tools that allows for inter-organism comparisons. This should enable the fission yeast community to take advantage of the large amount of available information on budding yeast transcriptome. New tools and ongoing developments are also presented here.

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Year:  2004        PMID: 14681424      PMCID: PMC308869          DOI: 10.1093/nar/gkh135

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


  17 in total

1.  Systematic determination of genetic network architecture.

Authors:  S Tavazoie; J D Hughes; M J Campbell; R J Cho; G M Church
Journal:  Nat Genet       Date:  1999-07       Impact factor: 38.330

2.  Functional discovery via a compendium of expression profiles.

Authors:  T R Hughes; M J Marton; A R Jones; C J Roberts; R Stoughton; C D Armour; H A Bennett; E Coffey; H Dai; Y D He; M J Kidd; A M King; M R Meyer; D Slade; P Y Lum; S B Stepaniants; D D Shoemaker; D Gachotte; K Chakraburtty; J Simon; M Bard; S H Friend
Journal:  Cell       Date:  2000-07-07       Impact factor: 41.582

3.  The KEGG databases at GenomeNet.

Authors:  Minoru Kanehisa; Susumu Goto; Shuichi Kawashima; Akihiro Nakaya
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

4.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

Authors:  Ron Edgar; Michael Domrachev; Alex E Lash
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

Review 5.  Toxicogenomics and drug discovery: will new technologies help us produce better drugs?

Authors:  Roger Ulrich; Stephen H Friend
Journal:  Nat Rev Drug Discov       Date:  2002-01       Impact factor: 84.694

6.  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

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

Authors:  M B Eisen; P T Spellman; P O Brown; D Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  1998-12-08       Impact factor: 11.205

8.  Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data.

Authors:  Rachel Lyne; Gavin Burns; Juan Mata; Chris J Penkett; Gabriella Rustici; Dongrong Chen; Cordelia Langford; David Vetrie; Jürg Bähler
Journal:  BMC Genomics       Date:  2003-07-10       Impact factor: 3.969

9.  Design and implementation of microarray gene expression markup language (MAGE-ML).

Authors:  Paul T Spellman; Michael Miller; Jason Stewart; Charles Troup; Ugis Sarkans; Steve Chervitz; Derek Bernhart; Gavin Sherlock; Catherine Ball; Marc Lepage; Marcin Swiatek; W L Marks; Jason Goncalves; Scott Markel; Daniel Iordan; Mohammadreza Shojatalab; Angel Pizarro; Joe White; Robert Hubley; Eric Deutsch; Martin Senger; Bruce J Aronow; Alan Robinson; Doug Bassett; Christian J Stoeckert; Alvis Brazma
Journal:  Genome Biol       Date:  2002-08-23       Impact factor: 13.583

10.  Website review: how to get the best from fission yeast genome data.

Authors:  Valerie Wood; Jürg Bähler
Journal:  Comp Funct Genomics       Date:  2002
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  4 in total

1.  GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.

Authors:  Philip Zimmermann; Matthias Hirsch-Hoffmann; Lars Hennig; Wilhelm Gruissem
Journal:  Plant Physiol       Date:  2004-09       Impact factor: 8.340

Review 2.  Cross species analysis of microarray expression data.

Authors:  Yong Lu; Peter Huggins; Ziv Bar-Joseph
Journal:  Bioinformatics       Date:  2009-04-08       Impact factor: 6.937

3.  Data mining tools for the Saccharomyces cerevisiae morphological database.

Authors:  Taro L Saito; Jun Sese; Yoichiro Nakatani; Fumi Sano; Masashi Yukawa; Yoshikazu Ohya; Shinichi Morishita
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

4.  Navigating public microarray databases.

Authors:  Christopher J Penkett; Jürg Bähler
Journal:  Comp Funct Genomics       Date:  2004
  4 in total

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