Database for exchangeable gene trap clones: Pathway and gene ontology analysis of exchangeable gene trap clone mouse lines
Database for exchangeable gene trap clones: Pathway and gene ontology analysis of exchangeable gene trap clone mouse lines
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DOI：
10.1111/dgd.12116
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发表时间：
2014-02-01
影响因子：
2.5
通讯作者：
Araki, Kimi
中科院分区：
文献类型：
--
作者：
Araki, Masatake;Nakahara, Mai;Araki, Kimi
胚胎干细胞中的基因捕获是一种成熟的小鼠基因组大规模随机插入突变的方法。我们已经建立了一个可交换的基因陷阱系统，其中一个报告基因可以交换任何其他感兴趣的DNA通过Cre/突变体lox介导的重组。我们分离了陷阱克隆，分析了陷阱基因，并构建了可交换基因陷阱克隆（EGTC）数据库[]。截至2013年8月31日，已登记的ES细胞系数量为1162个。我们还建立了454小鼠品系从陷阱ES克隆，并将它们存放在小鼠胚胎库中的动物资源和发展中心，熊本大学，日本。EGTC数据库是基因诱捕小鼠品系最广泛的学术资源。因为我们使用了启动子诱捕策略，所有诱捕的基因都在ES细胞中表达。为了了解EGTC文库中捕获基因的一般特征，我们使用京都基因和基因组百科全书（KEGG）进行通路分析，发现EGTC ES克隆涵盖了广泛的通路。我们还使用了小鼠基因组信息学（MGI）提供的基因本体论（GO）分类数据，以比较EGTC小鼠系中捕获的基因和MGI中注释的总基因之间每个GO术语中基因的功能分布。我们发现EGTC小鼠品系中捕获基因的功能分布和整个小鼠基因组的RefSeq基因的功能分布相似，表明EGTC小鼠品系捕获了广泛的小鼠基因。
Gene trapping in embryonic stem (ES) cells is a proven method for large-scale random insertional mutagenesis in the mouse genome. We have established an exchangeable gene trap system, in which a reporter gene can be exchanged for any other DNA of interest through Cre/mutant lox-mediated recombination. We isolated trap clones, analyzed trapped genes, and constructed the database for Exchangeable Gene Trap Clones (EGTC) []. The number of registered ES cell lines was 1162 on 31 August 2013. We also established 454 mouse lines from trap ES clones and deposited them in the mouse embryo bank at the Center for Animal Resources and Development, Kumamoto University, Japan. The EGTC database is the most extensive academic resource for gene-trap mouse lines. Because we used a promoter-trap strategy, all trapped genes were expressed in ES cells. To understand the general characteristics of the trapped genes in the EGTC library, we used Kyoto Encyclopedia of Genes and Genomes (KEGG) for pathway analysis and found that the EGTC ES clones covered a broad range of pathways. We also used Gene Ontology (GO) classification data provided by Mouse Genome Informatics (MGI) to compare the functional distribution of genes in each GO term between trapped genes in the EGTC mouse lines and total genes annotated in MGI. We found the functional distributions for the trapped genes in the EGTC mouse lines and for the RefSeq genes for the whole mouse genome were similar, indicating that the EGTC mouse lines had trapped a wide range of mouse genes.