A method for cross-species gene expression analysis with high-density oligonucleotide arrays
A method for cross-species gene expression analysis with high-density oligonucleotide arrays
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DOI：
10.1093/nar/gnh084
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发表时间：
2004-06-01
影响因子：
14.9
通讯作者：
Davis, S
中科院分区：
文献类型：
--
作者：
Ji, W;Zhou, WL;Davis, S
DNA微阵列已广泛应用于生物过程的基因表达分析。由于缺乏序列信息，其应用在很大程度上仅限于人类和少数模式生物。本研究中提供的是使用亲缘关系较远的哺乳动物物种（牛、猪和狗）与Affytelum人高密度寡核苷酸阵列或GeneChip（R）进行跨物种杂交的结果。基于AffyssingGeneChip（R）的独特特征，其中每个基因由多个探针代表，我们假设哺乳动物内的序列保守性足够高，以从一些探针产生足够的信号用于表达分析。我们证明，虽然整体杂交信号是低的跨物种杂交，大多数基因的一些探针仍然产生相当于同种杂交的信号。通过电子掩蔽杂交不良的探针，剩余的探针为基因表达分析提供了可靠的数据。我们开发了一种算法，利用GeneChip的匹配/错配特征选择可靠的探针进行分析。当使用所选探针比较两种组织之间的基因表达时，我们发现跨物种和同种杂交之间存在线性相关性。此外，我们使用随机选择的基因通过定量PCR验证了跨物种杂交结果。本文所示的方法可应用于植物和动物研究。
DNA microarrays have been widely used in gene expression analysis of biological processes. Due to a lack of sequence information, the applications have been largely restricted to humans and a few model organisms. Presented within this study are results of the cross-species hybridization with Affymetrix human high-density oligonucleotide arrays or GeneChip(R) using distantly related mammalian species; cattle, pig and dog. Based on the unique feature of the Affymetrix GeneChip(R) where every gene is represented by multiple probes, we hypothesized that sequence conservation within mammals is high enough to generate sufficient signals from some of the probes for expression analysis. We demonstrated that while overall hybridization signals are low for cross-species hybridization, a few probes of most genes still generated signals equivalent to the same-species hybridization. By masking the poorly hybridized probes electronically, the remaining probes provided reliable data for gene expression analysis. We developed an algorithm to select the reliable probes for analysis utilizing the match/mismatch feature of GeneChip(R). When comparing gene expression between two tissues using the selected probes, we found a linear correlation between the cross-species and same-species hybridization. In addition, we validated cross-species hybridization results by quantitative PCR using randomly selected genes. The method shown herein could be applied to both plant and animal research.