Table of Contents
Dataset Papers in Biology
Volume 2013, Article ID 706465, 7 pages
http://dx.doi.org/10.7167/2013/706465
Dataset Paper

Extending MapMan Ontology to Tobacco for Visualization of Gene Expression

1Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57007, USA
2Department of Zoology, The University of Melbourne, Parkville, VIC 5010, Australia
3Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA

Received 6 July 2012; Accepted 30 July 2012

Academic Editors: B. G. De Los Reyes, T. W. Nattkemper, and G. Ozsoyoglu

Copyright © 2013 Maurice H. T. Ling et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Microarrays are a large-scale expression profiling method which has been used to study the transcriptome of plants under various environmental conditions. However, manual inspection of microarray data is difficult at the genome level because of the large number of genes (normally at least 30 000) and the many different processes that occur within any given plant. MapMan software, which was initially developed to visualize microarray data for Arabidopsis, has been adapted to other plant species by mapping other species onto MapMan ontology. This paper provides a detailed procedure and the relevant computing codes to generate a MapMan ontology mapping file for tobacco (Nicotiana tabacum L.) using potato and Arabidopsis as intermediates. The mapping file can be used directly with our custom-made NimbleGen oligoarray, which contains gene sequences from both the tobacco gene space sequence and the tobacco gene index 4 (NTGI4) collection of ESTs. The generated dataset will be informative for scientists working on tobacco as their model plant by providing a MapMan ontology mapping file to tobacco, homology between tobacco coding sequences and that of potato and Arabidopsis, as well as adapting our procedure and codes for other plant species where the complete genome is not yet available.