GENEVESTIGATOR® Transcriptome Meta-Analysis and Biomarker Search Using Rice and Barley Gene Expression Databases
Philip Zimmermanna, Oliver Laule, Josy Schmitz, Tomas Hruz, Stefan Bleuler and Wilhelm Gruissem
Molecular Plant • Volume 1 • Number 5 • Pages 851–857
The wide-spread use of microarray technologies to study plant transcriptomes has led to important discov- eries and to an accumulation of profiling data covering a wide range of different tissues, developmental stages, pertur- bations, and genotypes. Querying a large number of microarray experiments can provide insights that cannot be gained by analyzing single experiments. However, such a meta-analysis poses significant challenges with respect to data comparability and normalization, systematic sample annotation, and analysis tools. GENEVESTIGATOR® addresses these issues using a large curated expression database and a set of specifically developed analysis tools that are accessible over the internet. This combination has already proven to be useful in the area of plant research based on a large set of Arabidopsis data (Grennan, 2006). Here, we present the release of the GENEVESTIGATOR® rice and barley gene expression databases that con- tain quality-controlled and well annotated microarray experiments using ontologies. The databases currently comprise experiments from pathology, plant nutrition, abiotic stress, hormone treatment, genotype, and spatial or temporal ana- lysis, but are expected to cover a broad variety of research areas as more experimental data become available. The tran- scriptome meta-analysis of the model species rice and barley is expected to deliver results that can be used for functional genomics and biotechnological applications in cereals.