Ling Maurice Ht, Rabara Roel C, Tripathi Prateek, Rushton Paul J, Ge Steven X
Department of Mathematics and Statistics, South Dakota State University, Brookings, South Dakota, USA 57007.
Dataset Pap Biol. 2013;2013. doi: 10.7167/2013/706465.
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 ( L.) using potato and Arabidopsis as intermediates. The mapping file can be used directly with our custom made NimbleGen oligoarray, that contains gene sequences from both the tobacco gene space sequence and the tobacco gene index 4 (NTGI4) collection of ESTs. The generated data set 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.
微阵列是一种大规模表达谱分析方法，已被用于研究各种环境条件下植物的转录组。然而，由于基因数量众多（通常至少30000个）以及任何给定植物体内发生的众多不同过程，在基因组水平上人工检查微阵列数据很困难。MapMan软件最初是为可视化拟南芥的微阵列数据而开发的，通过将其他物种映射到MapMan本体上，已被应用于其他植物物种。本文提供了一个详细的程序和相关计算代码，以马铃薯和拟南芥为中间物种生成烟草（Nicotiana tabacum L.）的MapMan本体映射文件。该映射文件可直接与我们定制的NimbleGen寡核苷酸阵列一起使用，该阵列包含来自烟草基因空间序列和烟草基因索引4（NTGI4）EST集合的基因序列。通过为烟草提供一个MapMan本体映射文件、烟草编码序列与马铃薯和拟南芥编码序列之间的同源性，以及将我们的程序和代码应用于尚未获得完整基因组的其他植物物种，生成的数据集将为以烟草为模式植物的科学家提供信息。
