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Visualization of the Arabidopsis MPSS data for five tissues: callus, flower, leaf, root, and silique

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fasta mpss

This page focuses on visualization of the project results. If you are looking for details of PyMood usage please refer to our bacterial project example.

MPSS stands for Massively Parallel Signature Sequencing, a technique invented and commercialized by Lynx Therapeutics, Inc. of Hayward, California. MPSS and related technologies have been described in publications by Brenner et al. (Nature Biotechnol. [2000] 18:630-634, and PNAS [2000] 97:1665-1670). Like SAGE (Serial Analysis of Gene Expression), MPSS produces short sequence signatures produced from a defined position within an mRNA, and the relative abundance of these signatures in a given library represents a quantitative estimate of expression of that gene. The MPSS signatures are 17 bp in length, and can uniquely identify >95% of all genes in Arabidopsis.

Software used

PyMood, MS Access, MS Excel, Netscape 7, MSIE 6

Project Implementation

1. The Arabidopsis MPSS database was stored and analyzed in MS Access.

2. Expression of MPSS unique tags from the TIGR annotated genes were compared for every pair of tissues. The expression data was exported from MS Access, normalized, and converted into .rgb format in MS Excel.

3. The data was visualized using PyMood. The .rgb files were opened in the PyMood 2D Viewer and saved as browsable images linked to the Arabidopsis MPSS database entries.

4. Unique tissue specific signatures were assigned to the genes, exported from MS Access, and converted into .rgb format in MS Excel. All tissue specific genes were assigned the same brightness, regardless of the expression level. The .rgb file was visualized in PyMood.

The Arabidopsis MPSS project is in public domain. The rest is copyright © 2001-2010 Allometra, LLC