%0 Journal Article
%T Arabidopsis Gene Family Profiler (aGFP) ¨C user-oriented transcriptomic database with easy-to-use graphic interface
%A Nikoleta Dupl'¨¢kov¨¢
%A David Re¨¾¨¢k
%A Patrik Hovanec
%A Barbora Honysov¨¢
%A David Twell
%A David Honys
%J BMC Plant Biology
%D 2007
%I BioMed Central
%R 10.1186/1471-2229-7-39
%X The Arabidopsis GFP database has been designed as an easy-to-use tool for users needing an easily accessible resource for expression data of single genes, pre-defined gene families or custom gene sets, with the further possibility of keyword search. Arabidopsis Gene Family Profiler presents a user-friendly web interface using both graphic and text output. Data are stored at the MySQL server and individual queries are created in PHP script. The most distinguishable features of Arabidopsis Gene Family Profiler database are: 1) the presentation of normalized datasets (Affymetrix MAS algorithm and calculation of model-based gene-expression values based on the Perfect Match-only model); 2) the choice between two different normalization algorithms (Affymetrix MAS4 or MAS5 algorithms); 3) an intuitive interface; 4) an interactive "virtual plant" visualizing the spatial and developmental expression profiles of both gene families and individual genes.Arabidopsis GFP gives users the possibility to analyze current Arabidopsis developmental transcriptomic data starting with simple global queries that can be expanded and further refined to visualize comparative and highly selective gene expression profiles.Completion and annotation of the Arabidopsis thaliana genome represented a major step in plant genetic research [1]. This knowledge enabled gene prediction, assignment of functional categories and gave an opportunity to study gene and chromosome organization including the distribution of transposable elements. Finally it has enabled the characterization of global gene expression patterns at the transcriptome level at different developmental stages and under various physiological and stress conditions. Efforts to reveal the biological functions of thousand of genes and their integration into proteome, metabolome and interactome networks has become the principal focus of many studies and represents key objective of the 2010 Project [2]A number of efficient and accurate gene expr
%U http://www.biomedcentral.com/1471-2229/7/39