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15000个独特的斑马鱼EST簇及其在微阵列中用于分析胚胎发育过程中基因表达模式的未来应用。

15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis.

作者信息

Lo Jane, Lee Sorcheng, Xu Min, Liu Feng, Ruan Hua, Eun Alvin, He Yawen, Ma Weiping, Wang Weefuen, Wen Zilong, Peng Jinrong

机构信息

Functional Genomics Lab, Institute of Molecular and Cell Biology, Singapore 117609.

出版信息

Genome Res. 2003 Mar;13(3):455-66. doi: 10.1101/gr.885403.

Abstract

A total of 15590 unique zebrafish EST clusters from two cDNA libraries have been identified. Most significantly, only 22% (3437) of the 15590 unique clusters matched 2805 (of 15200) clusters in the Danio rerio UniGene database, indicating that our EST set is complementary to the existing ESTs in the public database and will be invaluable in assisting the annotation of genes based on the upcoming zebrafish genome sequence. Blast search showed that 7824 of our unique clusters matched 6710 known or predicted proteins in the nonredundant database. A cDNA microarray representing approximately 3100 unique zebrafish cDNA clusters has been generated and used to profile the gene expression patterns across six different embryonic stages (cleavage, blastula, gastrula, segmentation, pharyngula, and hatching). Analysis of expression data using K-means clustering revealed that genes coding for muscle-specific proteins displayed similar expression patterns, confirming that the coordinate gene expression is important for myogenesis. Our results demonstrate that the combination of microarray technology with the zebrafish model system can provide useful information on how genes are coordinated in a genetic network to control zebrafish embryogenesis and can help to identify novel genes that are important for organogenesis.

摘要

从两个cDNA文库中总共鉴定出15590个独特的斑马鱼EST簇。最为显著的是,15590个独特簇中只有22%(3437个)与斑马鱼基因索引数据库中15200个簇中的2805个簇相匹配,这表明我们的EST集与公共数据库中现有的EST互补,对于基于即将到来的斑马鱼基因组序列辅助基因注释将具有极高价值。Blast搜索显示,我们的独特簇中有7824个与非冗余数据库中的6710个已知或预测蛋白质相匹配。已构建了一个代表约3100个独特斑马鱼cDNA簇的cDNA微阵列,并用于描绘六个不同胚胎阶段(卵裂期、囊胚期、原肠胚期、体节期、咽胚期和孵化期)的基因表达模式。使用K均值聚类分析表达数据表明,编码肌肉特异性蛋白质的基因呈现相似的表达模式,证实了协同基因表达对肌肉生成很重要。我们的结果表明,微阵列技术与斑马鱼模型系统相结合,能够提供有关基因如何在遗传网络中协同作用以控制斑马鱼胚胎发育的有用信息,并有助于识别对器官发生重要的新基因。

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