Summary
Massively parallel signature sequencing (MPSS) is a technology capable of sequencing simultaneously almost all the DNA molecules in a sample. This technology is well suited for deep profiling of mRNA and small RNA by the sequencing of cDNA tags. A series of mRNA MPSS databases has been created from various libraries derived from four different species (Arabidopsis, rice, grape, and Magnaporthe grisea, the rice blast fungus). Our mRNA MPSS databases measure the absolute expression level of most genes in the sample and provide information about potentially novel transcripts (antisense transcripts, alternative splice isoforms, and regulatory intergenic transcripts). In addition to these data, we have recently built an extensive database from MPSS-derived Arabidopsis small RNA samples. All the databases are accessible thorough our Web interface (http://mpss.udel.edu), and the individual pages are equipped with various graphical and analytical tools. Here, we focus on a subset of these tools (e.g., Gene Analysis [GA], Chromosome Viewer [CV], and Library Analysis [LIBAN]) and describe how the users can analyze and interpret our MPSS expression data.
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Acknowledgments
The authors thank Mayumi Nakano for helpful comments and critical reading of the manuscript. The tools and the databases described here were developed with support from the National Science Foundation Plant Genome Research Program.
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Nobuta, K., Vemaraju, K., Meyers, B.C. (2007). Methods for Analysis of Gene Expression in Plants Using MPSS. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology™, vol 406. Humana Press. https://doi.org/10.1007/978-1-59745-535-0_19
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DOI: https://doi.org/10.1007/978-1-59745-535-0_19
Publisher Name: Humana Press
Print ISBN: 978-1-58829-653-5
Online ISBN: 978-1-59745-535-0
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