Nieto-Díaz Manuel, Pita-Thomas Wolfgang, Nieto-Sampedro Manuel
Neural Plasticity Department, Instituto de Neurobiología Ramón y Cajal (CSIC), Madrid, Spain.
BMC Genomics. 2007 Apr 3;8:89. doi: 10.1186/1471-2164-8-89.
Gene expression profiles of non-model mammals may provide valuable data for biomedical and evolutionary studies. However, due to lack of sequence information of other species, DNA microarrays are currently restricted to humans and a few model species. This limitation may be overcome by using arrays developed for a given species to analyse gene expression in a related one, an approach known as "cross-species analysis". In spite of its potential usefulness, the accuracy and reproducibility of the gene expression measures obtained in this way are still open to doubt. The present study examines whether or not hybridization values from cross-species analyses are as reproducible as those from same-species analyses when using Affymetrix oligonucleotide microarrays.
The reproducibility of the probe data obtained hybridizing deer, Old-World primates, and human RNA samples to Affymetrix human GeneChip U133 Plus 2.0 was compared. The results show that cross-species hybridization affected neither the distribution of the hybridization reproducibility among different categories, nor the reproducibility values of the individual probes. Our analyses also show that a 0.5% of the probes analysed in the U133 plus 2.0 GeneChip are significantly associated to un-reproducible hybridizations. Such probes-called in the text un-reproducible probe sequences- do not increase in number in cross-species analyses.
Our study demonstrates that cross-species analyses do not significantly affect hybridization reproducibility of GeneChips, at least within the range of the mammal species analysed here. The differences in reproducibility between same-species and cross-species analyses observed in previous studies were probably caused by the analytical methods used to calculate the gene expression measures. Together with previous observations on the accuracy of GeneChips for cross-species analysis, our analyses demonstrate that cross-species hybridizations may provide useful gene expression data. However, the reproducibility and accuracy of these measures largely depends on the use of appropriated algorithms to derive the gene expression data from the probe data. Also, the identification of probes associated to un-reproducible hybridizations-useless for gene expression analyses- in the studied GeneChip, stress the need of a re-evaluation of the probes' performance.
非模式哺乳动物的基因表达谱可能为生物医学和进化研究提供有价值的数据。然而，由于缺乏其他物种的序列信息，DNA微阵列目前仅限于人类和少数模式物种。通过使用为特定物种开发的阵列来分析相关物种中的基因表达，可以克服这一限制，这种方法称为“跨物种分析”。尽管其具有潜在用途，但通过这种方式获得的基因表达测量的准确性和可重复性仍值得怀疑。本研究探讨了使用Affymetrix寡核苷酸微阵列时，跨物种分析的杂交值是否与同物种分析的杂交值一样具有可重复性。
比较了将鹿、旧世界灵长类动物和人类RNA样本与Affymetrix人类基因芯片U133 Plus 2.0杂交获得的探针数据再现性。结果表明，跨物种杂交既不影响不同类别之间杂交再现性的分布，也不影响单个探针的再现性值。我们的分析还表明，在U133 plus 2.0基因芯片中分析的0.5%的探针与不可再现的杂交显著相关。这种探针——文中称为不可再现探针序列——在跨物种分析中数量不会增加。
我们的研究表明，跨物种分析不会显著影响基因芯片的杂交再现性，至少在所分析的哺乳动物物种范围内如此。先前研究中观察到的同物种和跨物种分析之间再现性的差异可能是由用于计算基因表达测量的分析方法引起的。与先前关于基因芯片用于跨物种分析准确性的观察结果一起，我们的分析表明跨物种杂交可能提供有用的基因表达数据。然而，这些测量的再现性和准确性很大程度上取决于使用适当的算法从探针数据中得出基因表达数据。此外，在所研究的基因芯片中识别与不可再现杂交相关的探针——对基因表达分析无用——强调了重新评估探针性能的必要性。
