Held G A, Grinstein G, Tu Y
IBM TJ Watson Research Center, PO Box 218, Yorktown Heights, NY 10598, USA.
Nucleic Acids Res. 2006 May 24;34(9):e70. doi: 10.1093/nar/gkl122.
A theoretical study of the physical properties which determine the variation in signal strength from probe to probe on a microarray is presented. A model which incorporates probe-target hybridization, as well as the subsequent dissociation which occurs during stringent washing of the microarray, is introduced and shown to reasonably describe publicly available spike-in experiments carried out at Affymetrix. In particular, this model suggests that probe-target dissociation during the stringent wash plays a critical role in determining the observed hybridization intensities. In addition, it is demonstrated that non-specific hybridization introduces uncertainties which significantly limit the ability of any model to accurately quantify absolute gene expression levels while, in contrast, target folding appears to have little effect on these results. Finally, for data from target spike-in experiments, our model is shown to compare favorably with an existing statistical model in determining target concentration levels.
本文对决定微阵列上不同探针信号强度变化的物理性质进行了理论研究。引入了一个模型，该模型包含探针 - 靶标杂交以及微阵列严格洗涤过程中发生的后续解离，并证明其能够合理地描述在Affymetrix进行的公开可用的掺入实验。特别地，该模型表明，严格洗涤过程中的探针 - 靶标解离在确定观察到的杂交强度方面起着关键作用。此外，研究表明非特异性杂交会引入不确定性，这显著限制了任何模型准确量化绝对基因表达水平的能力，而相比之下，靶标折叠似乎对这些结果影响不大。最后，对于来自靶标掺入实验的数据，我们的模型在确定靶标浓度水平方面与现有的统计模型相比表现良好。
