ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.
ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.
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DOI：
10.1371/journal.pcbi.1002567
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发表时间：
2012
影响因子：
4.3
通讯作者：
Pollard KS
中科院分区：
文献类型：
--
作者：
Capra JA;Williams AG;Pollard KS
蛋白质的进化历史反映了其祖先的功能历史。最近的系统发育研究确定了不同的进化特征，蛋白质参与癌症，孟德尔疾病，和不同的个体发育阶段。尽管有可能深入了解蛋白质的细胞功能和相互作用，但很少进行这种比较系统发育分析，因为它们需要定制算法。我们开发了ProteinHistorian，以使广泛使用的蛋白质来源分析工具。给定感兴趣的蛋白质列表，ProteinHistorian估计每个蛋白质的系统发育年龄，量化特定年龄蛋白质的富集，并将蛋白质年龄的变化与其他蛋白质属性进行比较。ProteinHistorian允许灵活定义蛋白质年龄，包括几种算法，用于从不同的进化关系数据库中估计年龄。我们用三个例子来说明ProteinHistorian的使用。首先，我们证明了与黑猩猩和恒河猴相比，人类中高表达的蛋白质明显比人类特异性低表达的蛋白质年轻。接下来，我们发现具有注释调节功能的人类蛋白质明显比具有催化功能的蛋白质年轻。最后，我们比较了许多真核生物物种的蛋白质长度和年龄，正如以前的研究所预期的那样，发现蛋白质年龄和长度之间存在正相关，尽管通常很弱。ProteinHistorian可通过具有直观界面的Web服务器和一组命令行工具获得;这允许生物学家和生物信息学家将这些方法集成到他们的分析管道中。ProteinHistorian的模块化、可扩展设计促进了新数据集和算法的集成。ProteinHistorian网络服务器、源代码和32个真核生物基因组的预先计算的年龄可以在GNU公共许可下免费获得，网址是http://lighthouse.ucsf.edu/ProteinHistorian/。
The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight into the cellular functions and interactions of proteins, such comparative phylogenetic analyses are rarely performed, because they require custom algorithms. We developed ProteinHistorian to make tools for performing analyses of protein origins widely available. Given a list of proteins of interest, ProteinHistorian estimates the phylogenetic age of each protein, quantifies enrichment for proteins of specific ages, and compares variation in protein age with other protein attributes. ProteinHistorian allows flexibility in the definition of protein age by including several algorithms for estimating ages from different databases of evolutionary relationships. We illustrate the use of ProteinHistorian with three example analyses. First, we demonstrate that proteins with high expression in human, compared to chimpanzee and rhesus macaque, are significantly younger than those with human-specific low expression. Next, we show that human proteins with annotated regulatory functions are significantly younger than proteins with catalytic functions. Finally, we compare protein length and age in many eukaryotic species and, as expected from previous studies, find a positive, though often weak, correlation between protein age and length. ProteinHistorian is available through a web server with an intuitive interface and as a set of command line tools; this allows biologists and bioinformaticians alike to integrate these approaches into their analysis pipelines. ProteinHistorian's modular, extensible design facilitates the integration of new datasets and algorithms. The ProteinHistorian web server, source code, and pre-computed ages for 32 eukaryotic genomes are freely available under the GNU public license at http://lighthouse.ucsf.edu/ProteinHistorian/.
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基因本体论：2011年的增强。
影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
影响因子：
12.3
作者：
Capra JA;Pollard KS;Singh M
通讯作者：
Singh M
影响因子：
4.3
作者：
Reference Genome Group of the Gene Ontology Consortium
通讯作者：
Reference Genome Group of the Gene Ontology Consortium
影响因子：
5.8
作者：
Cohen, Ofir;Ashkenazy, Haim;Pupko, Tal
通讯作者：
Pupko, Tal
影响因子：
4.3
作者：
Kim WK;Marcotte EM
通讯作者：
Marcotte EM