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

by admin — last modified Apr 01, 2008 10:36 AM

For data produced by this project, go here.

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. This project, dubbed AtGenExpress, was funded by the DFG, and provided the Arabidopsis 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. In the spirit of other genome projects, raw data were released immediately and before publication.

The Affymetrix technology is also being made available to other groups, who can use the system for a nominal charge. Currently, outside users are hosted about once a month. In addition, the department is continuing to generate their own specific array data, which can all be found in ArrayExpress or NCBI GEO databases.

A tool for visualizing gene expression across development has been developed and can be accessed on our resource page, where one can also download various AtGenExpress datasets.