Automatic gene collection system for genome-scale overview of G-protein coupled receptors in Eukaryotes
Automatic gene collection system for genome-scale overview of G-protein coupled receptors in Eukaryotes
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DOI：
10.1016/j.gene.2005.05.038
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发表时间：
2005-12-30
期刊：
影响因子：
3.5
通讯作者：
Suwa, M
中科院分区：
文献类型：
--
作者：
Ono, Y;Fujibuchi, W;Suwa, M
我们已经开发了一个自动系统，用于从各种基因组中识别GPCR （g蛋白偶联受体）基因，并最终存储在SEVENS数据库（http://sevens.cbrc.jp/）中，该系统集成了基因查找器、序列比对工具、基序和结构域分配工具以及跨膜螺旋预测器等软件。SEVENS使我们能够使用具有高精度（99.4%灵敏度和96.6%特异性）的序列对“GPCR宇宙”进行基因组规模的概述。利用该系统，我们调查了7种真核生物和224种原核生物的全基因组，发现7种真核生物中有4 ~ 10 16个GPCR基因，而所有原核生物中只有16个GPCR基因。我们的初步结果表明，在人类、蝇类和线虫基因组中普遍存在A类家族、2类(B)家族、3类(C)家族和fz/smo家族11个亚家族。我们还利用Kolmogorov-Smimov检验分析了GPCR基因的染色体位置，发现物种特异性家族，如人类的嗅觉、味觉和趋化因子受体和线虫的趋化受体，倾向于广泛地形成簇状，而在蝇和植物基因组中没有发现明显的簇状。(C) 2005 Elsevier B.V.版权所有
We have developed an automatic system for identifying GPCR (G-protein coupled receptor) genes from various kinds of genomes, which is finally deposited in the SEVENS database (http://sevens.cbrc.jp/), by integrating such software as a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix predictor. SEVENS enables us to perform a genome-scale overview of the "GPCR universe" using sequences that are identified with high accuracy (99.4% sensitivity and 96.6% specificity). Using this system, we surveyed the complete genomes of 7 eukaryotes and 224 prokaryotes, and found that there are 4 to 10 16 GPCR genes in the 7 eukaryotes, and only a total of 16 GPCR genes in all the prokaryotes. Our preliminary results indicate that 11 subfamilies of the Class A family, the Class 2(B family, the Class 3(C) family and the fz/smo family are commonly found among human, fly, and nematode genomes. We also analyzed the chromosomal locations of the GPCR genes with the Kolmogorov-Smimov test, and found that species-specific families, such as olfactory, taste, and chemokine receptors in human and nematode chemoreceptor in worm, tend to form clusters extensively, whereas no significant clusters were detected in fly and plant genomes. (C) 2005 Elsevier B.V. All rights reserved.