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Extending MapMan Ontology to Tobacco for Visualization of Gene Expression

机译：将MapMan本体论扩展到烟草以实现基因表达的可视化

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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 forArabidopsis, 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 tabacumL.) using potato andArabidopsisas 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 andArabidopsis, as well as adapting our procedure and codes for other plant species where the complete genome is not yet available.
机译：微阵列是一种大规模表达谱分析方法，已用于研究各种环境条件下植物的转录组。但是，由于基因数量众多（通常至少30 000个）并且在给定植物中发生了许多不同的过程，因此在基因组水平上手动检查微阵列数据非常困难。 MapMan软件最初是为了可视化拟南芥的微阵列数据而开发的，现已通过将其他物种映射到MapMan本体上而适用于其他植物物种。本文提供了详细的过程和相关的计算代码，以使用马铃薯和拟南芥为中间体生成烟草（Nicotiana tabacumL。）的MapMan本体映射文件。映射文件可直接与我们定制的NimbleGen寡阵列一起使用，该阵列包含来自ESTs的烟草基因空间序列和烟草基因索引4（NTGI4）集合的基因序列。生成的数据集将通过提供MapMan本体映射文件到烟草，烟草编码序列与马铃薯和拟南芥的编码序列之间的同源性，以及针对其他植物物种修改我们的程序和代码，为从事烟草作为其模型植物研究的科学家提供参考。尚无完整的基因组。

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