Extending MapMan Ontology to Tobacco for Visualization of Gene Expression.
Extending MapMan Ontology to Tobacco for Visualization of Gene Expression.
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DOI：
10.7167/2013/706465
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发表时间：
2013-02
期刊：
影响因子：
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通讯作者：
M. Ling;R. Rabara;P. Tripathi;P. Rushton;S. X. Ge
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文献类型：
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作者：
M. Ling;R. Rabara;P. Tripathi;P. Rushton;S. X. Ge
基因芯片是一种大规模的表达谱分析方法，已被用于研究植物在各种环境条件下的转录组。然而，在基因组水平上手工检查微阵列数据是困难的，因为在任何给定的植物中都有大量的基因(通常至少是30,000个)和许多不同的过程。MapMan软件最初是为了将拟南芥的微阵列数据可视化而开发的，现在已经通过将其他物种映射到MapMan本体上而适用于其他植物物种。给出了生成烟草(Nictiana tabacum L.)MapMan本体映射文件的详细步骤和相关计算代码。以马铃薯和拟南芥为中间体。该图谱文件可以直接用于我们定制的NimbleGen寡核苷酸阵列，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。生成的数据集将为致力于将烟草作为他们的模式植物的科学家提供信息，方法是提供烟草的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，以及为尚未获得完整基因组的其他植物物种调整我们的程序和编码。
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, 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.