BATS: a Bayesian user-friendly software for analyzing time series microarray experiments.
BATS: a Bayesian user-friendly software for analyzing time series microarray experiments.
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DOI：
10.1186/1471-2105-9-415
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发表时间：
2008-10-06
影响因子：
3
通讯作者：
Pensky M
中科院分区：
文献类型：
--
作者：
Angelini C;Cutillo L;De Canditiis D;Mutarelli M;Pensky M
给定细胞中的基因表达水平可能受到不同因素的影响，即药理学或医学治疗。对于不同的基因，对给定刺激的反应通常不同，并且可能取决于时间。现代分子生物学的目标之一是高通量鉴定与特定治疗或感兴趣的生物过程相关的基因。从方法和计算的角度来看，分析高维时间过程的微阵列数据需要非常具体的工具，通常不包括在标准的软件包。最近，本文的作者开发了一个完全贝叶斯方法，它允许一个识别差异表达的基因在一个“单样本”的时间过程的微阵列实验，排名和估计他们的表达谱。该方法是基于显式表达式的计算，因此，非常计算效率。本文介绍的软件包BATS（贝叶斯时间序列分析）实现了上述方法。它允许用户自动识别和排名差异表达的基因，并估计其表达谱时，至少有5-6个时间点可用。该软件包具有用户友好的界面。BATS成功地解决了时间进程微阵列实验中出现的各种技术难题，如少量观察、非均匀采样间隔和重复或缺失数据。BATS是一个免费的用户友好的软件，用于分析模拟和真实的微阵列时间过程实验。该软件、用户手册和一个简短的说明性示例可在最佳可行技术服务网站上免费获得：
Gene expression levels in a given cell can be influenced by different factors, namely pharmacological or medical treatments. The response to a given stimulus is usually different for different genes and may depend on time. One of the goals of modern molecular biology is the high-throughput identification of genes associated with a particular treatment or a biological process of interest. From methodological and computational point of view, analyzing high-dimensional time course microarray data requires very specific set of tools which are usually not included in standard software packages. Recently, the authors of this paper developed a fully Bayesian approach which allows one to identify differentially expressed genes in a 'one-sample' time-course microarray experiment, to rank them and to estimate their expression profiles. The method is based on explicit expressions for calculations and, hence, very computationally efficient. The software package BATS (Bayesian Analysis of Time Series) presented here implements the methodology described above. It allows an user to automatically identify and rank differentially expressed genes and to estimate their expression profiles when at least 5–6 time points are available. The package has a user-friendly interface. BATS successfully manages various technical difficulties which arise in time-course microarray experiments, such as a small number of observations, non-uniform sampling intervals and replicated or missing data. BATS is a free user-friendly software for the analysis of both simulated and real microarray time course experiments. The software, the user manual and a brief illustrative example are freely available online at the BATS website:
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DOI：
10.1073/pnas.091062498
发表时间：
2001-04-24
影响因子：
11.1
作者：
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DOI：
10.1111/j.2517-6161.1995.tb02031.x
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1995-01-01
影响因子：
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影响因子：
3
作者：
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DOI：
10.1073/pnas.0504609102
发表时间：
2005-09-06
影响因子：
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