Time squared: repeated measures on phylogenies.
Time squared: repeated measures on phylogenies.
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时间平方：系统发育的重复测量。
DOI：
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发表时间：
2006
影响因子：
10.7
通讯作者：
M. Suchard
中科院分区：
文献类型：
--
作者：
Hua Guo;R. Weiss;X. Gu;M. Suchard
基因表达谱响应外部扰动的研究产生重复的测量数据，通常遵循非线性曲线。为了探索跨基因家族的这些特征的进化，我们引入了系统发育重复测量（PR）模型。这些模型从数据中的两种形式的相关性中汲取力量。通过基因复制，家族的进化关系产生了第一种形式。第二个是在分类单位中，在这个例子中，个体基因在时间点上的相关性。我们借用布朗扩散过程沿着给定的系统发育树来解释相关性，并采用重复测量框架来模拟后者。通过模拟研究，我们证明了重复测量模型优于先前可用的方法，即使用偏差信息标准作为贝叶斯模型选择工具，将纵向观测或其差异视为独立和同分布；在适当的情况下，借用系统发育信息的PR模型也比非系统发育的重复测量模型表现得更好。然后，我们分析了酵母激酶家族基因表达的进化，使用样条估算了3个扰动实验中的非线性行为。同样，PR模型优于以前的方法，并提供祖先表达谱的预测。为了更普遍地证明PR模型的适用性，我们对4种灵长类动物的大脑发育变异进行了简短的研究。
Studies of gene expression profiles in response to external perturbation generate repeated measures data that generally follow nonlinear curves. To explore the evolution of such profiles across a gene family, we introduce phylogenetic repeated measures (PR) models. These models draw strength from 2 forms of correlation in the data. Through gene duplication, the family's evolutionary relatedness induces the first form. The second is the correlation across time points within taxonic units, individual genes in this example. We borrow a Brownian diffusion process along a given phylogenetic tree to account for the relatedness and co-opt a repeated measures framework to model the latter. Through simulation studies, we demonstrate that repeated measures models outperform the previously available approaches that consider the longitudinal observations or their differences as independent and identically distributed by using deviance information criteria as Bayesian model selection tools; PR models that borrow phylogenetic information also perform better than nonphylogenetic repeated measures models when appropriate. We then analyze the evolution of gene expression in the yeast kinase family using splines to estimate nonlinear behavior across 3 perturbation experiments. Again, the PR models outperform previous approaches and afford the prediction of ancestral expression profiles. To demonstrate PR model applicability more generally, we conclude with a short examination of variation in brain development across 4 primate species.
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影响因子：
10.7
作者：
Gu, ZL;Cavalcanti, A;Li, WH
通讯作者：
Li, WH
影响因子：
56.9
作者：
Chu, S;DeRisi, J;Herskowitz, I
通讯作者：
Herskowitz, I
影响因子：
56.9
作者：
DeRisi, JL;Iyer, VR;Brown, PO
通讯作者：
Brown, PO
影响因子：
3.3
作者：
Gasch, AP;Spellman, PT;Brown, PO
通讯作者：
Brown, PO