Arabidopsis MPSS. An online resource for quantitative expression analysis.

We have developed a public Web-based resource to facilitate access to global expression data for Arabidopsis, available at http://mpss.udel.edu/at. Developing an understanding of patterns and levels of transcriptional activity is the starting point for analyzing individual genes or gene families. Genome-wide transcriptional analyses are also revealing the relationship between the structure and organization of a genome and the activity of the genes encoded in that genome. Whole-genome expression data can be obtained from a variety of technologies, including cDNA microarrays (DeRisi et al., 1997), oligonucleotide microarrays (Lockhart et al., 1996), serial analysis of gene expression (SAGE; Velculescu et al., 1995), and massively parallel signature sequencing (MPSS; Brenner et al., 2000a, 2000b). The diversity of microarray platforms, improving densities, relatively low cost per experiment, and the range of technologies (e.g. cDNA, short oligo, and long oligo) have made it easier for labs to obtain their own microarray data than to reanalyze publicly-released data. Tag-based expression data like SAGE and MPSS are more easily utilized by multiple labs because the data format is relatively standard, the genes that are analyzed are not preselected, and the per-library cost discourages unnecessary duplication of experiments. While online resources have been described for SAGE data (Lash et al., 2000; Ball et al., 2001), MPSS data have several unique aspects and must be treated in a different way than SAGE data (Meyers et al., 2004a). None of the existing Web sites for tag-based expression data are customized in a way that links plant genomic and expression data. We have developed a public, Web-based resource for the analysis of gene expression in the model plant, Arabidopsis. The database and interface is specialized to store and facilitate public access to gene expression data derived by MPSS. Our database currently contains more than 36,991,173 17-base sequence signatures and more than 31,404,553 20-base signatures derived by MPSS from more than 14 Arabidopsis libraries (Meyers et al., 2004a). The MPSS data and Arabidopsis genomic sequence and annotation were used as the basis for the development of publiclyavailable analysis and comparison tools. Our Web site (http://mpss.udel.edu/at) includes a genome viewer, a set of gene, signature, and library analysis pages, an FTP site for retrieval of the data, and a signature extraction tool to allow specific sequence comparisons to the MPSS data. In this report, we describe the development, organization, and utility of this resource.