An important type of heterosis, known as hybrid vigor, refers to the enhancements in the phenotype of hybrid progeny relative to their inbred parents. Although hybrid vigor is extensively utilized in agriculture, its molecular basis is still largely unknown. In an effort to understand phenotypic heterosis at the molecular level, researchers are measuring transcript abundance levels of thousands of genes in parental inbred lines and their hybrid offspring using RNA sequencing (RNA-seq) technology. The resulting data allow researchers to search for evidence of gene expression heterosis as one potential molecular mechanism underlying heterosis of agriculturally important traits. The null hypotheses of greatest interest in testing for gene expression heterosis are composite null hypotheses that are difficult to test with standard statistical approaches for RNA-seq analysis. To address these shortcomings, we develop a hierarchical negative binomial model and draw inferences using a computationally tractable empirical Bayes approach to inference. We demonstrate improvements over alternative methods via a simulation study based on a maize experiment and then analyze that maize experiment with our newly proposed methodology. This article has supplementary material online.

中文翻译：

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用于检测基因表达杂种优势的RNA-seq数据的经验贝叶斯分析。

杂种优势的一种重要类型，称为杂种活力，是指杂种后代的表型相对于其近交亲本的增强。尽管杂种优势在农业中得到广泛利用，但其分子基础仍是未知之数。为了在分子水平上理解表型杂种优势，研究人员正在使用RNA测序（RNA-seq）技术测量亲本近交系及其杂交后代中数千个基因的转录本丰度水平。由此产生的数据使研究人员可以寻找基因表达杂种优势的证据，这是潜在的农业重要性状杂种优势的潜在分子机制。在测试基因表达杂种优势中最受关注的零假设是复合零假设，这些复合零假设很难用RNA-seq分析的标准统计方法进行检验。为了解决这些缺点，我们开发了一个分层的负二项式模型，并使用可计算的易处理的经验贝叶斯方法进行推理。我们通过基于玉米实验的模拟研究证明了替代方法的改进，然后使用我们新提出的方法对玉米实验进行了分析。本文在线提供了补充材料。我们通过基于玉米实验的模拟研究证明了替代方法的改进，然后使用我们新提出的方法对玉米实验进行了分析。本文在线提供了补充材料。我们通过基于玉米实验的模拟研究证明了替代方法的改进，然后使用我们新提出的方法对玉米实验进行了分析。本文在线提供了补充材料。