Genomic gene clustering analysis of pathways in eukaryotes
Genomic gene clustering analysis of pathways in eukaryotes
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DOI：
10.1101/gr.737703
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发表时间：
2003-05-01
期刊：
影响因子：
7
通讯作者：
Sonnhammer, ELL
中科院分区：
文献类型：
--
作者：
Lee, JM;Sonnhammer, ELL
由于转录操纵子，在原核生物中通常发现通路中基因的基因组聚类，但这些在大多数真核生物中不存在。然而，在真核生物基因组中可能存在较小程度的通路成员聚集，这些通路成员有助于一组功能合作基因的共调节。我们分析了五个测序的真核生物基因组，用于在KEGG数据库中分配到相同途径的基因聚类。基因组中98%至30%的分析途径被发现表现出比偶然预期的显着更高的聚类水平。按聚类水平降序排列，研究的基因组是酿酒酵母、智人、秀丽隐杆线虫、拟南芥和黑腹果蝇。令人惊讶的是，基因组之间在哪些途径最聚集方面并没有太多的一致性。在所有物种中发现的69种途径中，只有7种在所有5种途径中显着聚集。这种物种特异性的途径聚类模式可能反映了特定谱系特有的适应或进化事件。我们注意到，虽然操纵子在线虫中很常见，但只有58%的通路显示出显著的聚类，这比人类中的要少。S.酿酒酵母表现出显著的聚类。
Genomic clustering of genes in a pathway is commonly found in prokaryotes due to transcriptional operons, but these are not present in most eukaryotes. Yet, there might be clustering to a lesser extent of pathway members in eukaryotic genomes, that assist coregulation of a set of functionally cooperating genes. We analyzed five sequenced eukaryotic genomes for clustering of genes assigned to the same pathway in the KEGG database. Between 98% and 30% of the analyzed pathways in a genome were found to exhibit significantly higher clustering levels than expected by chance. in descending order by the level of clustering, the genomes studied were Saccharomyces cerevisiae, Homo sapiens, Caenorhabditis elegans, Arabidopsis thaliana, and Drosophila melanogaster. Surprisingly, there is not much agreement between genomes in terms of which pathways are most clustered. Only seven of 69 pathways found in all species were significantly clustered in all five of them. This species-specific pattern of pathway clustering may reflect adaptations or evolutionary events unique to a particular lineage. We note that although operons are common in C elegans, only 58% of the pathways showed significant clustering, which is less than in human. Virtually all pathways in S. cerevisiae showed significant clustering.