The COG database: an updated version includes eukaryotes.
The COG database: an updated version includes eukaryotes.
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COG数据库：更新版本包括真核生物。
DOI：
10.1186/1471-2105-4-41
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发表时间：
2003-09-11
影响因子：
3
通讯作者：
Natale, DA
中科院分区：
文献类型：
--
作者：
Tatusov, RL;Fedorova, ND;Jackson, JD;Jacobs, AR;Kiryutin, B;Koonin, EV;Krylov, DM;Mazumder, R;Mekhedov, SL;Nikolskaya, AN;Rao, BS;Smirnov, S;Sverdlov, AV;Vasudevan, S;Wolf, YI;Yin, JJ;Natale, DA
原核生物和真核生物多个基本完整的基因组序列的可用性，激发了构建这些基因组基因进化分类的需求和机会。这种基于基因间直系同源关系的分类系统似乎是比较基因组学的一个自然框架，应该有助于基因组的功能注释和大规模的进化研究。
我们在此描述了先前开发的从原核生物和单细胞真核生物测序基因组中描绘蛋白质直系同源簇（COGs）的系统的一次重大更新，以及7个真核基因组预测直系同源簇的构建，我们将其命名为真核直系同源组（KOGs）。COG集合目前包含138,458种蛋白质，它们形成4873个COGs，占66个单细胞生物基因组中编码的185,505种（预测）蛋白质的75%。真核直系同源组（KOGs）包括来自7个真核基因组的蛋白质：3种动物（线虫秀丽隐杆线虫、果蝇黑腹果蝇和智人）、1种植物拟南芥、2种真菌（酿酒酵母和粟酒裂殖酵母）以及细胞内微孢子虫寄生虫兔脑炎微孢子虫。当前的KOG集合由4852个直系同源簇组成，其中包括59,838种蛋白质，约占所分析的110,655种真核基因产物的54%。与COGs对原核生物基因组的覆盖相比，能被纳入KOGs的真核基因比例要小得多；预计新的真核基因组的加入将使KOGs对真核基因组的覆盖大幅增加。对KOGs的系统发育模式的研究揭示了一个在所有分析物种中都存在的保守核心，约占KOG集合的20%。KOG集合的这个保守部分比COG集合的普遍存在部分（约占COGs的1%）大得多。部分原因可能是所包含的真核基因组数量较少，但这也可能反映了真核生物作为一个分支的相对紧密性以及真核基因组更大的进化稳定性。
原核生物和真核生物直系同源蛋白质集合的更新版本有望成为对新测序基因组（包括复杂真核生物的基因组）进行功能注释以及全基因组进化研究的有用平台。
The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens), one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe), and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (~1% of the COGs). In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes. The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies.
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影响因子：
7
作者：
Lecompte, O;Ripp, R;Poch, O
通讯作者：
Poch, O
影响因子：
7
作者：
Lespinet, O;Wolf, YI;Aravind, L
通讯作者：
Aravind, L
DOI：
10.2307/2412448
发表时间：
1970-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FITCH, WM
通讯作者：
FITCH, WM
影响因子：
3.6
作者：
Koonin, EV;Mushegian, AR;Walker, DR
通讯作者：
Walker, DR
影响因子：
56.9
作者：
Goffeau, A;Barrell, BG;Oliver, SG
通讯作者：
Oliver, SG