Measuring gene expression divergence: the distance to keep.
Measuring gene expression divergence: the distance to keep.
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DOI：
10.1186/1745-6150-5-51
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发表时间：
2010-08-06
期刊：
影响因子：
5.5
通讯作者：
Mushegian A
中科院分区：
文献类型：
--
作者：
Glazko G;Mushegian A
基因表达差异是一种表型特征，反映了基因调控的进化，并表征了物种之间以及同一物种内细胞和组织之间的差异。已经提出了几种距离度量，如欧几里得距离和基于相关性的距离来度量表达分歧。我们表明，不同的距离度量确定了基因表达模式的不同趋势。当比较8个大鼠和人类组织中的同源基因时，欧几里德距离确定在表达背景附近的所有组织中统一表达的基因是表达模式最保守的基因。相比之下，基于相关性的距离和广义平均距离将同源组织中具有一致变化的基因识别为最保守的基因。另一方面，基于相关性的距离、欧几里得距离和广义平均距离很好地突出了物种间同源组织中的基因表达模式与物种内非同源组织相比具有较高的相似性。高维数字数据中存在不同的趋势，为了突出特定的趋势，需要选择适当的距离度量。用于测量表达差异的距离度量的选择可以由特定研究中感兴趣的表达模式来决定。本文由Mikhail Gelfand，Eugene Koning和Subhajyoti de(Sarah Teichmann提名)审阅。
Gene expression divergence is a phenotypic trait reflecting evolution of gene regulation and characterizing dissimilarity between species and between cells and tissues within the same species. Several distance measures, such as Euclidean and correlation-based distances have been proposed for measuring expression divergence. We show that different distance measures identify different trends in gene expression patterns. When comparing orthologous genes in eight rat and human tissues, the Euclidean distance identified genes uniformly expressed in all tissues near the expression background as genes with the most conserved expression pattern. In contrast, correlation-based distance and generalized-average distance identified genes with concerted changes among homologous tissues as those most conserved. On the other hand, correlation-based distance, Euclidean distance and generalized-average distance highlight quite well the relatively high similarity of gene expression patterns in homologous tissues between species, compared to non-homologous tissues within species. Different trends exist in the high-dimensional numeric data, and to highlight a particular trend an appropriate distance measure needs to be chosen. The choice of the distance measure for measuring expression divergence can be dictated by the expression patterns that are of interest in a particular study. This article was reviewed by Mikhail Gelfand, Eugene Koonin and Subhajyoti De (nominated by Sarah Teichmann).
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DOI：
10.1073/pnas.2636460100
发表时间：
2003-01-07
影响因子：
11.1
作者：
Rogen, P;Fain, B
通讯作者：
Fain, B
影响因子：
3.3
作者：
Pereira, Vini;Waxman, David;Eyre-Walker, Adam
通讯作者：
Eyre-Walker, Adam
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：
2.1
作者：
Irizarry, RA;Hobbs, B;Speed, TP
通讯作者：
Speed, TP
影响因子：
3
作者：
Rossnes, R;Eidhammer, I;Liberles, DA
通讯作者：
Liberles, DA