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MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters

Philip J Law1, Clotilde Claudel-Renard13, Fourie Joubert1, Abraham I Louw1 and Dave K Berger2*

Author Affiliations

1 Bioinformatics and Computational Biology Unit, African Centre for Gene Technologies (ACGT), Department of Biochemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, 0002, South Africa

2 Department of Plant Science, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa

3 Laboratoire de Biologie Cellulaire et Moléculaire, Biogemma, Domaine de Sandreau, 31700, Mondonville, France

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BMC Genomics 2008, 9:105  doi:10.1186/1471-2164-9-105

Published: 28 February 2008

Abstract

Background

Microarray technology makes it possible to identify changes in gene expression of an organism, under various conditions. Data mining is thus essential for deducing significant biological information such as the identification of new biological mechanisms or putative drug targets. While many algorithms and software have been developed for analysing gene expression, the extraction of relevant information from experimental data is still a substantial challenge, requiring significant time and skill.

Description

MADIBA (MicroArray Data Interface for Biological Annotation) facilitates the assignment of biological meaning to gene expression clusters by automating the post-processing stage. A relational database has been designed to store the data from gene to pathway for Plasmodium, rice and Arabidopsis. Tools within the web interface allow rapid analyses for the identification of the Gene Ontology terms relevant to each cluster; visualising the metabolic pathways where the genes are implicated, their genomic localisations, putative common transcriptional regulatory elements in the upstream sequences, and an analysis specific to the organism being studied.

Conclusion

MADIBA is an integrated, online tool that will assist researchers in interpreting their results and understand the meaning of the co-expression of a cluster of genes. Functionality of MADIBA was validated by analysing a number of gene clusters from several published experiments – expression profiling of the Plasmodium life cycle, and salt stress treatments of Arabidopsis and rice. In most of the cases, the same conclusions found by the authors were quickly and easily obtained after analysing the gene clusters with MADIBA.