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AGNS - Arabidopsis GeneNet supplementary


NAR Molecular Biology Database Collection entry number 636
Omelyanchuk N.1, Mironova V.1, Poplavsky A.1, Podkoldny N.1, Kolchanov N.1, Mjolsness E.2 and Meyerowitz E.3
1Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
2Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92607, USA
3Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA

Database Description

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.

References

1. Ananko EA, Podkolodny NL, Stepanenko IL, Podkolodnaya OA, Rasskazov DA, Miginsky DS, Likhoshvai VA, Ratushny AV, Podkolodnaya NN, Kolchanov NA. (2005) GeneNet in 2005. Nucleic Acids Res. 33: D425-D427.
2. Wellmer F, Riechmann JL, Alves-Ferreira M, Meyerowitz EM. (2004) Genome-wide analysis of spatial gene expression in Arabidopsis flowers. Plant Cell 16: 1314-1326.

3. Kolchanov NA, Nedosekina EA, Ananko EA, Likhoshvai VA, Podkolodny NL, Ratushny AV, Stepanenko IL, Podkolodnaya OA, Ignatieva EV, Matushkin YG. (2002) GeneNet database: description and modeling of gene networks. In Silico Biol. 2: 97-110.

Category: Plant databases
Subcategory: Arabidopsis thaliana

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