Dynamics of dendritic cell maturation are identified through a novel filtering strategy applied to biological time-course microarray replicates.
Dynamics of dendritic cell maturation are identified through a novel filtering strategy applied to biological time-course microarray replicates.
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DOI：
10.1186/1471-2172-11-41
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发表时间：
2010-08-03
期刊：
影响因子：
3
通讯作者：
Fetrow JS
中科院分区：
文献类型：
--
作者：
Olex AL;Hiltbold EM;Leng X;Fetrow JS
树突状细胞（DC）在原发性免疫应答中起核心作用，并在经历关键的成熟过程后成为适应性免疫应答的强有力刺激物。了解DC成熟的动力学将为这一重要过程提供关键见解。时间进程微阵列实验可以提供独特的见解DC成熟动力学。重复实验是必要的，以解决实验和生物变异性的问题。统计方法和平均值通常用于识别重要信号。在这里，提出了一种新的策略，用于过滤的重复时间过程的微阵列数据，它确定重复之间的一致信号，并施加到DC时间过程的微阵列实验。DC成熟的时间动力学通过用poly（I：C）刺激DC并在1至24小时的5个时间点进行基因表达来研究。新的过滤策略使用标准的统计学和倍数变化技术，沿着重复时间曲线的一致性，以鉴定在两个生物重复实验中一致的差异表达基因。为了解决集群再现性的问题，一个共识聚类方法，确定集群的基因，其表达在重复之间的变化一致，也被开发和应用。对所得簇的分析揭示了DC成熟的许多已知和新的特征，例如特异性免疫应答途径的上调。有趣的是，更多的基因被下调而不是上调。结果确定了一个更全面的程序下调，包括许多基因参与蛋白质合成，代谢和管家需要维持细胞的完整性和代谢。新的过滤策略强调了分析微阵列数据时一致性和可重复性结果的重要性，并利用重复实验之间的一致性作为特征选择和聚类的标准，而无需平均或以其他方式组合重复数据。在DC成熟过程中观察到显著的下调程序表明DC正在为细胞死亡做准备，并提供了更好地理解该过程的途径。这种新的过滤策略可以适用于分析其他大规模的时间过程数据集的重复。
Dendritic cells (DC) play a central role in primary immune responses and become potent stimulators of the adaptive immune response after undergoing the critical process of maturation. Understanding the dynamics of DC maturation would provide key insights into this important process. Time course microarray experiments can provide unique insights into DC maturation dynamics. Replicate experiments are necessary to address the issues of experimental and biological variability. Statistical methods and averaging are often used to identify significant signals. Here a novel strategy for filtering of replicate time course microarray data, which identifies consistent signals between the replicates, is presented and applied to a DC time course microarray experiment. The temporal dynamics of DC maturation were studied by stimulating DC with poly(I:C) and following gene expression at 5 time points from 1 to 24 hours. The novel filtering strategy uses standard statistical and fold change techniques, along with the consistency of replicate temporal profiles, to identify those differentially expressed genes that were consistent in two biological replicate experiments. To address the issue of cluster reproducibility a consensus clustering method, which identifies clusters of genes whose expression varies consistently between replicates, was also developed and applied. Analysis of the resulting clusters revealed many known and novel characteristics of DC maturation, such as the up-regulation of specific immune response pathways. Intriguingly, more genes were down-regulated than up-regulated. Results identify a more comprehensive program of down-regulation, including many genes involved in protein synthesis, metabolism, and housekeeping needed for maintenance of cellular integrity and metabolism. The new filtering strategy emphasizes the importance of consistent and reproducible results when analyzing microarray data and utilizes consistency between replicate experiments as a criterion in both feature selection and clustering, without averaging or otherwise combining replicate data. Observation of a significant down-regulation program during DC maturation indicates that DC are preparing for cell death and provides a path to better understand the process. This new filtering strategy can be adapted for use in analyzing other large-scale time course data sets with replicates.
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DOI：
10.1126/science.1179050
发表时间：
2009-10-09
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Amit I;Garber M;Chevrier N;Leite AP;Donner Y;Eisenhaure T;Guttman M;Grenier JK;Li W;Zuk O;Schubert LA;Birditt B;Shay T;Goren A;Zhang X;Smith Z;Deering R;McDonald RC;Cabili M;Bernstein BE;Rinn JL;Meissner A;Root DE;Hacohen N;Regev A
通讯作者：
Regev A
影响因子：
4.4
作者：
Bertho, N;Blancheteau, VM;Mooney, N
通讯作者：
Mooney, N
影响因子：
4.2
作者：
Bain, Vincent G.;Yoshida, Eric M.;Subramanian, G. Mani
通讯作者：
Subramanian, G. Mani
影响因子：
64.5
作者：
Garrett, WS;Chen, LM;Mellman, I
通讯作者：
Mellman, I
影响因子：
3.8
作者：
Espert, L;Degols, G;Mechti, N
通讯作者：
Mechti, N