Genetical genomics:: use all data
Genetical genomics:: use all data
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DOI：
10.1186/1471-2164-8-69
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发表时间：
2007-03-12
期刊：
影响因子：
4.4
通讯作者：
Bahamonde, Antonio
中科院分区：
文献类型：
--
作者：
Perez-Enciso, Miguel;Quevedo, Jose R.;Bahamonde, Antonio
背景：遗传基因组学是阐明复杂性状和疾病易感性基础的一个非常有力的工具。尽管它的相关性，然而，表达数量性状基因座（eQTL）的统计建模并没有得到应有的重视。基于两个合理的断言（i）一个好的模型应该考虑所有可用的变量作为潜在的影响，（ii）基因表达是高度相互关联的，我们建议eQTL模型应该考虑其余的表达水平作为潜在的回归，除了markers.Results：它表明，权力可以增加这种策略。我们还表明，使用经典的统计和支持向量机技术在重新分析的公共数据，外部成绩单，即。例如，除了被分析的转录本之外，转录本平均比标记物本身解释更多的变异性。eQTL热点的存在根据这些结果进行了重新评估。结论：模型选择是遗传基因组学研究中一个关键但被忽视的问题。虽然我们还远没有一个通用的策略，在这方面的模型选择，我们至少可以提出，任何转录水平扫描不仅为标记基因分型，但也为其余的基因表达水平。可以使用某种逐步回归策略来选择最终模型。
Background: Genetical genomics is a very powerful tool to elucidate the basis of complex traits and disease susceptibility. Despite its relevance, however, statistical modeling of expression quantitative trait loci (eQTL) has not received the attention it deserves. Based on two reasonable assertions (i) a good model should consider all available variables as potential effects, and (ii) gene expressions are highly interconnected, we suggest that an eQTL model should consider the rest of expression levels as potential regressors, in addition to the markers.Results: It is shown that power can be increased with this strategy. We also show, using classical statistical and support vector machines techniques in a reanalysis of public data, that the external transcripts, i. e., transcripts other than the one being analysed, explain on average much more variability than the markers themselves. The presence of eQTL hotspots is reassessed in the light of these results.Conclusion: Model choice is a critical yet neglected issue in genetical genomics studies. Although we are far from having a general strategy for model choice in this area, we can at least propose that any transcript level is scanned not only for the markers genotyped but also for the rest of gene expression levels. Some sort of stepwise regression strategy can be used to select the final model.