Correlation between sequence conservation and the genomic context after gene duplication.
Correlation between sequence conservation and the genomic context after gene duplication.
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DOI：
10.1093/nar/gki913
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发表时间：
2005
影响因子：
14.9
通讯作者：
Snel B
中科院分区：
文献类型：
--
作者：
Notebaart RA;Huynen MA;Teusink B;Siezen RJ;Snel B
可靠基因功能预测的比较基因组学的关键并发症是研究基因重复的基因的存在。两种基因组（即对这些重复的基因的内核），我们研究了在序列水平上最相似的基因尽管大多数研究的病例显示出序列相似性和基因 - 邻次保存之间的一致模式，但大量的比例为29-38％，这并不一致。在内部杂物之间，这似乎是由于两个与直系同源物的序列进化率非常相似的偶然结果需要一对一的直系关系，建议将上下文信息（即，原核生物中的基因 - 邻居和真核生物的共表达）与蛋白质序列信息相结合，以预测在存在异子群落的情况下最可能的功能等效性直系同源物。
A key complication in comparative genomics for reliable gene function prediction is the existence of duplicated genes. To study the effect of gene duplication on function prediction, we analyze orthologs between pairs of genomes where in one genome the orthologous gene has duplicated after the speciation of the two genomes (i.e. inparalogs). For these duplicated genes we investigate whether the gene that is most similar on the sequence level is also the gene that has retained the ancestral gene-neighborhood. Although the majority of investigated cases show a consistent pattern between sequence similarity and gene-neighborhood conservation, a substantial fraction, 29–38%, is inconsistent. The observation of inconsistency is not the result of a chance outcome owing to a lack of divergence time between inparalogs, but rather it seems to be the result of a chance outcome caused by very similar rates of sequence evolution of both inparalogs relative to their ortholog. If one-to-one orthologous relationships are required, it is advisable to combine contextual information (i.e. gene-neighborhood in prokaryotes and co-expression in eukaryotes) with protein sequence information to predict the most probable functional equivalent ortholog in the presence of inparalogs.
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DOI：
10.1073/pnas.0409186102
发表时间：
2005-01-18
影响因子：
11.1
作者：
Gu, X;Zhang, ZQ;Huang, W
通讯作者：
Huang, W
影响因子：
3.2
作者：
MAROLDA, CL;VALVANO, MA
通讯作者：
VALVANO, MA
影响因子：
13.8
作者：
Dandekar, T;Snel, B;Bork, P
通讯作者：
Bork, P
影响因子：
14.9
作者：
Snel, B;van Noort, V;Huynen, MA
通讯作者：
Huynen, MA
影响因子：
3.6
作者：
Metzner, M;Germer, J;Hengge, R
通讯作者：
Hengge, R