Inter-species differences of co-expression of neighboring genes in eukaryotic genomes.
Inter-species differences of co-expression of neighboring genes in eukaryotic genomes.
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DOI：
10.1186/1471-2164-5-4
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发表时间：
2004-01-13
期刊：
影响因子：
4.4
通讯作者：
Kohane IS
中科院分区：
文献类型：
--
作者：
Fukuoka Y;Inaoka H;Kohane IS
越来越多的证据表明真核生物基因组内的基因顺序不是随机的。在酵母和蠕虫中，相邻或邻近基因倾向于共表达。在人类、蠕虫和果蝇中发现了共表达基因的聚类。然而，在小鼠和大鼠中，尚未研究染色体距离（CD）对共表达的影响。此外，到目前为止还没有进行过跨物种比较。我们利用酵母、果蝇、蠕虫、大鼠、小鼠和人6种真核生物的表达数据分析了CD和归一化距离（ND）的影响。我们分析了来自6个物种的24组表达数据。高共表达对被分类到CD间隔大小相等的箱中，并计算每个箱中的共表达率（CoER）。在所有数据集中，在近距离CD范围内获得的CoER高于远距离CD范围。这些结果表明，在所有研究物种中，CD对共表达的影响是一致的。然而，使用ND的结果显示出更大的多样性。CoER的种内和种间比较表明，邻近基因的共表达率在种间存在显著差异。一对BLAST分析发现8 - 30%的高共表达对是重复基因。我们证实，在六个真核生物物种中，有一个一致的趋势，即邻近基因可能共表达。配对BLAST结果表明，非重复对对共表达有显著影响。CD和ND的比较表明CD的优势作用。
There is increasing evidence that gene order within the eukaryotic genome is not random. In yeast and worm, adjacent or neighboring genes tend to be co-expressed. Clustering of co-expressed genes has been found in humans, worm and fruit flies. However, in mice and rats, an effect of chromosomal distance (CD) on co-expression has not been investigated yet. Also, no cross-species comparison has been made so far. We analyzed the effect of CD as well as normalized distance (ND) using expression data in six eukaryotic species: yeast, fruit fly, worm, rat, mouse and human. We analyzed 24 sets of expression data from the six species. Highly co-expressed pairs were sorted into bins of equal sized intervals of CD, and a co-expression rate (CoER) in each bin was calculated. In all datasets, a higher CoER was obtained in a short CD range than a long distance range. These results show that across all studied species, there was a consistent effect of CD on co-expression. However, the results using the ND show more diversity. Intra- and inter-species comparisons of CoER reveal that there are significant differences in the co-expression rates of neighboring genes among the species. A pair-wise BLAST analysis finds 8 – 30 % of the highly co-expressed pairs are duplic ated genes. We confirmed that in the six eukaryotic species, there was a consistent tendency that neighboring genes are likely to be co-expressed. Results of pair-wised BLAST indicate a significant effect of non-duplicated pairs on co-expression. A comparison of CD and ND suggests the dominant effect of CD.
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影响因子：
30.8
作者：
Armstrong, SA;Staunton, JE;Korsmeyer, SJ
通讯作者：
Korsmeyer, SJ
影响因子：
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Roy, PJ;Stuart, JM;Kim, SK
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Kim, SK
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22.4
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RYAN, TA
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RYAN, TA
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Alizadeh, AA;Eisen, MB;Staudt, LM
通讯作者：
Staudt, LM
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64.8
作者：
Pomeroy, SL;Tamayo, P;Golub, TR
通讯作者：
Golub, TR