Comparison of computational methods for the identification of cell cycle-regulated genes
Comparison of computational methods for the identification of cell cycle-regulated genes
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DOI：
10.1093/bioinformatics/bti093
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发表时间：
2005-04-01
期刊：
影响因子：
5.8
通讯作者：
Brunak, S
中科院分区：
文献类型：
--
作者：
de Lichtenberg, U;Jensen, LJ;Brunak, S
动机：DNA微阵列已被广泛用于研究细胞周期的转录程序在一些模式生物。酿酒酵母的数据，特别是已经进行了广泛的生物信息学分析方法，旨在确定正确的和完整的一套定期表达的genes.Results：在这里，我们提供了第一个彻底的基准，这种方法，令人惊讶地揭示，最新的和更先进的数学方法实际上执行差的分析发表与原始的微阵列数据集。我们表明，这种准确性的损失特别影响的方法，只模拟的表达谱的形状，而不考虑调控的幅度。我们提出了一个简单的基于置换的方法，比大多数现有的方法更好地执行。
Motivation: DNA microarrays have been used extensively to study the cell cycle transcription programme in a number of model organisms. The Saccharomyces cerevisiae data in particular have been subjected to a wide range of bioinformatics analysis methods, aimed at identifying the correct and complete set of periodically expressed genes.Results: Here, we provide the first thorough benchmark of such methods, surprisingly revealing that most new and more mathematically advanced methods actually perform worse than the analysis published with the original microarray data sets. We show that this loss of accuracy specifically affects methods that only model the shape of the expression profile without taking into account the magnitude of regulation. We present a simple permutation-based method that performs better than most existing methods.