Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA

MPSS (massively parallel signature sequencing) is a sequencing-based technology that uses a unique method to quantify gene expression level, generating millions of short sequence tags per library. We have created a series of databases for four species (Arabidopsis, rice, grape and Magnaporthe grisea, the rice blast fungus). Our MPSS databases measure the expression level of most genes under defined conditions and provide information about potentially novel transcripts (antisense transcripts, alternative splice isoforms and regulatory intergenic transcripts). A modified version of MPSS has been used to perform deep profiling of small RNAs from Arabidopsis, and we have recently adapted our database to display these data. Interpretation of the small RNA MPSS data is facilitated by the inclusion of extensive repeat data in our genome viewer. All the data and the tools introduced in this article are available at

Images from the ‘Gene Analysis’ output pages showing the annotated UTR regions and exons for the gene, along with the associated genomic signatures

<p><b>Copyright information:</b></p><p>Taken from "Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA"</p><p>Nucleic Acids Research 2005;34(Database issue):D731-D735.</p><p>Published online 28 Dec 2005</p><p>PMCID:PMC1347440.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> This example has only one exon, and UTRs are indicated with pink shading. All the signatures are linked to the Signature Analysis page. () Viewer with small RNA signatures (black triangles pointing toward the DNA) and repetitive sequences (in this example, a retrotransposon-related repeat is shown as a pink block in the background). () Viewer with mRNA data only (mRNA signatures appear as colored triangles parallel to the DNA)