Phosphoregulators: Protein kinases and protein phosphatases of mouse
Phosphoregulators: Protein kinases and protein phosphatases of mouse
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DOI：
10.1101/gr.954803
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发表时间：
2003-06-01
期刊：
影响因子：
7
通讯作者：
Grimmond, S
中科院分区：
文献类型：
--
作者：
Forrest, ARR;Ravasi, T;Grimmond, S
随着人类和小鼠基因组序列的完成，现在的任务转向识别它们的编码转录本和分配基因功能。在这项研究中，我们已经进行了计算的方法来识别和分类所有的蛋白激酶和磷酸酶存在于小鼠基因互补。通过挖掘Ensembl基因预测和公开可用的cDNA序列与一组InterPro结构域产生了这些序列的非冗余集。该方法鉴定了561种候选蛋白激酶和162种候选蛋白磷酸酶。然后使用TribeMCL蛋白质序列相似性聚类，然后CLUSTALV比对和分层树生成来分析该群组。这种方法使我们能够（1）区分蛋白激酶和磷酸酶家族的真正成员和相关生物化学的酶，（2）确定家族的结构，（3）提出以前未表征的成员的功能。通过这种方法获得的分类与以前的计划，并允许我们展示域协会与一些集群的良好协议。最后，我们评论的互补性质的cDNA和基因组为基础的基因检测和FANTOM 2转录组项目的影响。
With the completion of the human and mouse genome sequences, the task now turns to identifying their encoded transcripts and assigning gene function. In this study, we have undertaken a computational approach to identify and classify all of the protein kinases and phosphatases present in the mouse gene complement. A nonredundant set of these sequences was produced by mining Ensembl gene predictions and publicly available cDNA sequences with a panel of InterPro domains. This approach identified 561 candidate protein kinases and 162 candidate protein phosphatases. This cohort was then analyzed using TribeMCL protein sequence similarity clustering followed by CLUSTALV alignment and hierarchical tree generation. This approach allowed us to (1) distinguish between true members of the protein kinase and phosphatase families and enzymes of related biochemistry, (2) determine the structure of the families, and (3) suggest functions for previously uncharacterized members. The classifications obtained by this approach were in good agreement with previous schemes and allowed us to demonstrate domain associations with a number of clusters. Finally, we comment on the complementary nature of cDNA and genome-based gene detection and the impact of the FANTOM2 transcriptome project.