AGNS—A Database on Expression of Arabidopsis Genes

  • N. Omelyanchuk
  • V. Mironova
  • A. Poplavsky
  • N. Podkoldny
  • N. Kolchanov
  • E. Mjolsness
  • E. Meyerowitz

Abstract

AGNS (Arabidopsis GeneNet supplementary database) is an Internet-available resource that provides access to description of the functions of the known Arabidopsis genes at various levels—the levels of mRNA, protein, cell, tissue, and ultimately at the levels of organs and the organism in both wild type and mutant backgrounds. AGNS annotates published papers on gene expression and function and by this way integrates, systematizes, and classifies this heterogeneous, disparate, and scattered information. AGNS consists of three databases—the Expression Database (ED), the Phenotype Database (PD), and the Reference Database (RD)—and two controlled vocabularies. ED describes gene expression in wild type, mutants, and transgenic plants; PD contains information on phenotypic abnormalities in mutant and transgenic plants; and RD includes references to the papers and description of plant growth conditions with an indication of the ecotypes used as control in the experiments. Detailed controlled vocabularies on growth stages and morphology were developed around the annotated data. AGNS makes possible the search for genes expressed in particular organs, at particular stages, for genes whose expression is altered in particular mutants, for alleles causing particular phenotypic abnormalities, and for pleiotropic effect of particular mutations. Navigation table and search tools are used to browse the informational content of the database and controlled vocabularies.

Key words

Arabidopsis gene expression phenotype database mutant transgenic plants 

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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • N. Omelyanchuk
    • 1
  • V. Mironova
    • 1
  • A. Poplavsky
    • 1
  • N. Podkoldny
    • 1
  • N. Kolchanov
    • 1
  • E. Mjolsness
    • 2
  • E. Meyerowitz
    • 3
  1. 1.Institute of Cytology and GeneticsSiberian Branch of the Russian Academy of SciencesNovosibirskRussia
  2. 2.Institute for Genomics and Bioinformatics; Bren School of Information and Computer SciencesUniversity of CaliforniaIrvineUSA
  3. 3.Division of BiologyCalifornia Institute of TechnologyPasadenaUSA

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