Database

Arabidopsis Gene Family Profiler (aGFP) – user-oriented transcriptomic database with easy-to-use graphic interface

Nikoleta Dupl'áková^1,2 , David Reňák^1,2,3 , Patrik Hovanec⁴ , Barbora Honysová⁵ , David Twell⁶ and David Honys^1,2

¹ Laboratory of Pollen Biology, Institute of Experimental Botany ASCR v.v.i., Rozvojová 263, 165 00 Prague 6, Czech Republic

²Department of Plant Physiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic

³Department of Plant Physiology and Anatomy, Faculty of Biological Sciences, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic

⁴Krymská 8/122, 101 00 Praha 10, Czech Republic

⁵Laboratory of Cell Biology, Institute of Experimental Botany ASCR v.v.i., Rozvojová 263, 165 00 Prague 6, Czech Republic

⁶Department of Biology, University of Leicester, Leicester, LE1 7RH, UK

author email corresponding author email

BMC Plant Biology 2007, 7:39doi:10.1186/1471-2229-7-39

Published:	23 July 2007

Abstract

Background

Microarray technologies now belong to the standard functional genomics toolbox and have undergone massive development leading to increased genome coverage, accuracy and reliability. The number of experiments exploiting microarray technology has markedly increased in recent years. In parallel with the rapid accumulation of transcriptomic data, on-line analysis tools are being introduced to simplify their use. Global statistical data analysis methods contribute to the development of overall concepts about gene expression patterns and to query and compose working hypotheses. More recently, these applications are being supplemented with more specialized products offering visualization and specific data mining tools. We present a curated gene family-oriented gene expression database, Arabidopsis Gene Family Profiler (aGFP; http://agfp.ueb.cas.cz webcite), which gives the user access to a large collection of normalised Affymetrix ATH1 microarray datasets. The database currently contains NASC Array and AtGenExpress transcriptomic datasets for various tissues at different developmental stages of wild type plants gathered from nearly 350 gene chips.

Results

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.

Conclusion

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.