Modeling oligonucleotide microarray signals.
Modeling oligonucleotide microarray signals.
复制标题
DOI：
10.2165/00822942-200605030-00003
复制
发表时间：
2006-01-01
期刊：
影响因子：
--
通讯作者：
Zhang, Jiong
中科院分区：
文献类型：
--
作者：
Zhang, Yongqing;Ferreira, Antonio;Zhang, Jiong
化学原理表明，在DNA微阵列表面上，一个目标与其互补探针的特异性结合，以及其他核苷酸片段与相同探针之间的非特异性结合，是相互竞争的。我们证明这种机制可以通过考虑在微阵列表面发生的竞争性化学反应来理解。受Zhang和Hekstra开创性工作的启发，我们基于可能的反应机制开发了用于微阵列信号分析的物理模型，并使用并行，通用，模拟退火算法实现了该模型。使用Affymetrix拉丁平方峰值实验提供的数据，我们的模型显示了良好的拟合数据。预测表达水平与测试转录本的峰值浓度之间的相关性证明了我们的模型具有良好的预测能力。
Chemical principles dictate that the specific binding of a target to its complementary probes on a DNA microarray surface, and the nonspecific binding between other nucleotide segments and the same probes, are mutually competitive. We demonstrate that this mechanism can be understood by considering the competitive chemical reaction taking place on the microarray surface. Inspired by the pioneering work of Zhang and Hekstra, we have developed a physical model for microarray signal analysis, based on possible reaction mechanisms, and implemented it with a parallel, generic, simulated-annealing algorithm. Using data supplied by the Affymetrix Latin-square spike-in experiments, our model showed excellent fitting of the data. This correlation between the predicted expression levels and the spike-in concentrations of test transcripts demonstrated good predictive abilities of our model.