Utilizing microarray spot characteristics to improve cross-species hybridization results
Utilizing microarray spot characteristics to improve cross-species hybridization results
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DOI：
10.1016/j.ygeno.2007.06.008
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发表时间：
2007-11-01
期刊：
影响因子：
4.4
通讯作者：
Koltai, Hinanit
中科院分区：
文献类型：
--
作者：
Bar-Or, Canniya;Novikov, Eugene;Koltai, Hinanit
跨物种杂交（CSH），即，一种（目标）物种RNA与代表另一种（参照）物种的DNA微阵列杂交，通常用于研究物种多样性。然而，必须应用CSH数据的过滤来提取有效信息。我们提出了一种新的方法来过滤CSH数据，它利用斑点特征（SC）的图像定量数据从扫描斑点cDNA微阵列。鉴定了受探针和靶序列之间的序列相似性影响的五个SC（指定为BS-SC）。通过所有五个BS-SC阈值的过滤证明了三个检查实验中的两个的改进的聚类，这表明BS-SC可以用于过滤通过CSH获得的数据，以提高结果的有效性。这种CSH数据过滤方法可能成为研究各种物种的一种有前途的工具，特别是当目标物种没有基因组信息时。(c)2007年爱思唯尔公司All rights reserved.
Cross-species hybridization (CSH), i.e., the hybridization of a (target) species RNA to a DNA microarray that represents another (reference) species, is often used to study species diversity. However, filtration of CSH data has to be applied to extract valid information. We present a novel approach to filtering the CSH data, which utilizes spot characteristics (SCs) of image-quantification data from scanned spotted cDNA microarrays. Five SCs that were affected by sequence similarity between probe and target sequences were identified (designated as BS-SCs). Filtration by all five BS-SC thresholds demonstrated improved clustering for two of the three examined experiments, suggesting that BS-SCs may serve for filtration of data obtained by CSH, to improve the validity of the results. This CSH data-filtration approach could become a promising tool for studying a variety of species, especially when no genomic information is available for the target species. (c) 2007 Elsevier Inc. All rights reserved.