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

Nikoleta Dupl'Áková,David Twell,David Honys,Patrik Hovanec,Barbora Honysová,David Reňák

doi:10.1186/1471-2229-7-39

Abstract

BackgroundMicroarray 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; ), 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.ResultsThe 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.ConclusionArabidopsis 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.

Highlights

Microarray technologies belong to the standard functional genomics toolbox [12,13] and have undergone massive development leading to increased genome coverage, accuracy and reliability
In this article we introduce Arabidopsis Gene Family Profiler, a web-based gene expression database with visualization tools
The first subset contains data obtained within a scope of the AtGenExpress project [59], the second comprises all other datasets deposited at Nottingham Arabidopsis Stock Centre (NASC) and was labeled NASCArrays [26]

Summary

Introduction

Microarray technologies belong to the standard functional genomics toolbox and have undergone massive development leading to increased genome coverage, accuracy and reliability. 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. For the discovery of partial or whole gene functional or regulatory networks, the development of high-throughput technologies is essential with genome-wide transcriptomic studies providing a major input [3] Several such methods have been developed including, cDNA fingerprinting [4], serial analysis of gene expression – SAGE [5], massively parallel signature sequencing – MPSS [6], high-density DNA oligonucleotide probe microarrays [7,8] or cDNA arrays [9]. The introduction of the Minimum Information About Microarray experiments (MIAME) as standard documentation for array experiments and in transcriptomic databases, increasing the value and comparability of microarray data [15]

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Conclusion