The aim of the project is to develop new approaches to the analysis of Arabidopsis microarray data. The project is a collaboration between the Molecular Plant Sciences Group in the Institute of Biomedical and Life Sciences (A. Amtmann, R. Breitling), the Sir Henry Wellcome Functional Genomics Facility (P. Herzyk), the Department of Statistics (E. Wit), and the Bioinformatics Research Centre (R. Breitling, P. Herzyk).
By examining the transcriptional response of Arabidopsis thaliana plants to a variety of nutrient and environmental stress conditions we want to identify novel mechanisms that allow plants to cope under adverse conditions. To this end we will develop new statistical approaches to identify significantly regulated genes from genome-wide datasets, and implement techniques that allow convenient integration of biological, evolutionary, and biochemical information with expression data obtained from microarrays.
Experimental results are available as a searchable database supplement accompanying a paper by Armengaud, Breitling & Amtmann (2004). This paper also contains the first comprehensive application of the analysis tools developed in this project to a large plant dataset.
In the context of this project we have recently implemented new techniques for the analysis of microarrays at the SHWFGF. References and software downloads are available at the GlaMA website.
R. Breitling has prepared a short summary of general conclusions for the design of microarray experiments.
Status: Finished. Duration: April 2003 for 2 years, funded by the BBSRC.
Breitling R, Amtmann A, Herzyk P (2004):
Iterative Group Analysis (iGA): A simple tool to enhance sensitivity
and facilitate interpretation of microarray experiments.
BMC Bioinformatics 5: 34.
[PubMed]
Breitling R, Amtmann A, Herzyk P (2004):
Graph-based iterative Group Analysis enhances microarray interpretation.
BMC Bioinformatics 5: 100.
[PubMed]
Breitling R, Armengaud P, Amtmann A, Herzyk P (2004):
Rank products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments.
FEBS Letters 573: 83-92.
[Supplement]
Armengaud P, Breitling R, Amtmann A (2004):
The potassium-dependent transcriptome of Arabidopsis thaliana
reveals a prominent role of jasmonic acid in nutrient signaling.
Plant Physiol. 136: 2556–2576.
[PubMed]
[Supplementary Webpage]