AtGenExpress expression atlas of Arabidopsis thaliana (Laubinger, Schmid, Weigel)

The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. Hence, a long-term goal of research in the department is to understand the transcriptional code, i.e., the combinatorial relationship between the binding of transcription factors to DNA and the resulting production of RNA in the correct location and amounts. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, the department played a lead role in an international effort to develop a gene expression atlas of Arabidopsis thaliana. This project, dubbed AtGenExpress, was funded by the DFG, and provided the community with access to a large set of Affymetrix microarray data. As part of this collaboration, the department generated expression data from 79 different samples analyzed in triplicate. The focus in Tübingen was on different tissues and different developmental stages, while other groups were studying the effects of biotic and abiotic stress, hormones and different light conditions.

Subsequently, we have been using Affymetrix tiling arrays to interrrogate the genes not found on the ATH1 expression array, in the At-TAX project.

Most recently, we have established RNA-seq -- transcriptome sequencing -- using the Illumina platform. The advantage of RNA-seq is that it does not require prior knowledge of a genome. In addition, it has the potential to be more quantitative (although statistical issues have not been completely resolved).

Our own specific array data, which can all be found in ArrayExpress or NCBI GEO databases.

Tools for visualizing AtGenExpress and At-TAX data can be accessed on our resource page, where one can also download various datasets.

Personnel

Dr. Sascha Laubinger

Postdoc with DFG grant for own position

Dr. Stefan Henz

Staff scientist in bioinformatics

Dr. Markus Schmid

Group leader

Dr. Detlef Weigel

Director

Key publications

• Laubinger, S., Zeller, G., Henz, S. R., Sachsenberg, T., Widmer, C. K., Naouar, N., Vuylsteke, M., Schölkopf, B., Rätsch G., and Weigel, D. (2008) At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol. 9, R112.
• Schmid, M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron, M., Schölkopf, B., Weigel, D., and Lohmann, J. (2005) A gene expression map of Arabidopsis development. Nature Genetics 37, 501-506.

• Zeller, G., Henz, S., Widmer, C. K., Sachsenberg. T., Rätsch. R., Weigel, D., and Laubinger, S. (2009) Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole genome tiling arrays. Plant J. 58, 1068-1082.