Evans Kenneth, Ott Sascha, Hansen Annika, Koentges Georgy, Wernisch Lorenz
School of Crystallography, Birkbeck College, Malet Street, London, UK.
BMC Bioinformatics. 2007 Mar 2;8:71. doi: 10.1186/1471-2105-8-71.
S/MARs are regions of the DNA that are attached to the nuclear matrix. These regions are known to affect substantially the expression of genes. The computer prediction of S/MARs is a highly significant task which could contribute to our understanding of chromatin organisation in eukaryotic cells, the number and distribution of boundary elements, and the understanding of gene regulation in eukaryotic cells. However, while a number of S/MAR predictors have been proposed, their accuracy has so far not come under scrutiny.
We have selected S/MARs with sufficient experimental evidence and used these to evaluate existing methods of S/MAR prediction. Our main results are: 1.) all existing methods have little predictive power, 2.) a simple rule based on AT-percentage is generally competitive with other methods, 3.) in practice, the different methods will usually identify different sub-sequences as S/MARs, 4.) more research on the H-Rule would be valuable.
A new insight is needed to design a method which will predict S/MARs well. Our data, including the control data, has been deposited as additional material and this may help later researchers test new predictors.
支架/基质附着区域（S/MARs）是DNA中附着于核基质的区域。已知这些区域会对基因表达产生重大影响。S/MARs的计算机预测是一项极具意义的任务，有助于我们理解真核细胞中的染色质组织、边界元件的数量和分布，以及真核细胞中的基因调控。然而，尽管已经提出了多种S/MAR预测器，但到目前为止，它们的准确性尚未受到审查。
我们选择了有充分实验证据的S/MARs，并以此来评估现有的S/MAR预测方法。我们的主要结果如下：1）所有现有方法的预测能力都很弱；2）基于AT百分比的简单规则通常与其他方法具有竞争力；3）在实际应用中，不同方法通常会将不同的子序列识别为S/MARs；4）对H规则进行更多研究将很有价值。
需要新的思路来设计一种能很好地预测S/MARs的方法。我们的数据，包括对照数据，已作为补充材料存档，这可能有助于后来的研究人员测试新的预测器。
