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首页> 外文期刊>The Journal of toxicological sciences >Comparison of gene expression profiles among papilla, medulla and cortex in rat kidney.
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Comparison of gene expression profiles among papilla, medulla and cortex in rat kidney.

机译：大鼠肾脏乳头，髓质和皮质之间基因表达谱的比较。

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The aim of this study was to compare gene expression profiles in the different kidney regions as the basis for toxicogenomics. Rat kidney was separated into papilla, medulla and cortex, and total RNA was isolated from these and from the whole slice. Gene expression profiling was performed using Affymetrix Rat Genome 230 2.0 Array. When global normalization was applied, the expression of beta-actin or GAPDH varied among the regions. It was considered that such a comparison could not be made, especially between papilla and other portions, since the production of total mRNA in the former was relatively low. In fact, ANOVA was performed on the gene expression values with global normalization in papilla, medulla, cortex, and whole slice, and the numbers of genes appeared to be the highest in papilla. It was also observed that many genes showed their maximum or minimum in the whole slice, which was theoretically impossible. To overcome the problems associated with global normalization, the "percelome" normalization (a way to obtain the values directly related to the copies of mRNA per cell) was employed to compare the regions. In applying this procedure, probe sets with regional difference in expression were efficiently extracted by ANOVA. When they were sorted by the fold difference to other regions, the higher rank was occupied by genes characteristic of the functions of kidney, i.e., channels, transporters and metabolic enzymes. Some of them were consistent with the literature and were related to pathophysiological phenomena. Comprehensive comparison of data of gene expression in the renal anatomical area will greatly enhance studies of the physiological function and mechanism of toxicity in kidney.
机译：这项研究的目的是比较不同肾脏区域的基因表达谱，作为毒理基因组学的基础。将大鼠肾脏分为乳头，髓质和皮层，并从这些以及整个切片中分离出总RNA。使用Affymetrix Rat Genome 230 2.0 Array进行基因表达谱分析。当应用全局归一化时，β-肌动蛋白或GAPDH的表达在区域之间变化。认为不能进行这种比较，特别是在乳头和其他部分之间，因为前者中总mRNA的产生相对较低。实际上，在乳头，髓质，皮层和整个切片中对基因表达值进行了总体标准化的ANOVA，并且基因数量似乎在乳头中最高。还观察到许多基因在整个切片中显示出其最大值或最小值，这在理论上是不可能的。为了克服与全局归一化相关的问题，采用“ percelome”归一化（一种获得与每个细胞的mRNA拷贝直接相关的值的方法）来比较区域。在应用该程序时，通过ANOVA有效地提取了表达区域差异的探针集。当通过与其他区域的倍数差异对它们进行分类时，具有肾脏功能特征的基因即通道，转运蛋白和代谢酶占据了较高的排名。其中一些与文献一致，并且与病理生理现象有关。肾脏解剖区域中基因表达数据的全面比较将大大加强对肾脏的生理功能和毒性机制的研究。

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