A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus.
A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus.
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DOI：
10.1093/nar/gkj413
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发表时间：
2006
影响因子：
14.9
通讯作者：
Tomlinson, CR
中科院分区：
文献类型：
--
作者：
Sartor, MA;Zorn, AM;Schwanekamp, JA;Halbleib, D;Karyala, S;Howell, ML;Dean, GE;Medvedovic, M;Tomlinson, CR
最近对大量热带爪蟾表达序列进行的测序使得开发出一种高通量方法来研究爪蟾整体 RNA 基因表达。我们检查了具有历史意义的非洲爪蟾模型系统和日益使用的非洲爪蟾模型系统之间的全局基因表达相似性和差异，并评估了热带爪蟾微阵列平台是否可用于非洲爪蟾。这些密切相关的物种还被用来研究一个更普遍的问题：mRNA 序列差异和基因表达水平差异之间是否存在关联？我们利用非洲小蠹和热带小蠹不同组织和发育阶段的微阵列对全局基因表达谱进行了全面比较。我们 (i) 表明 X.tropicalis 探针为 X.laevis 提供了有效的微阵列平台，(ii) 描述了比较种间 mRNA 图谱的方法，以纠正杂交效率的差异，(iii) 显示独立于杂交偏倚，随着 X.laevis 和 X.tropicalis 之间 mRNA 序列差异的增加，mRNA 表达水平的差异也会增加。
The recent sequencing of a large number of Xenopus tropicalis expressed sequences has allowed development of a high-throughput approach to study Xenopus global RNA gene expression. We examined the global gene expression similarities and differences between the historically significant Xenopus laevis model system and the increasingly used X.tropicalis model system and assessed whether an X.tropicalis microarray platform can be used for X.laevis. These closely related species were also used to investigate a more general question: is there an association between mRNA sequence divergence and differences in gene expression levels? We carried out a comprehensive comparison of global gene expression profiles using microarrays of different tissues and developmental stages of X.laevis and X.tropicalis. We (i) show that the X.tropicalis probes provide an efficacious microarray platform for X.laevis, (ii) describe methods to compare interspecies mRNA profiles that correct differences in hybridization efficiency and (iii) show independently of hybridization bias that as mRNA sequence divergence increases between X.laevis and X.tropicalis differences in mRNA expression levels also increase.
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