Pellegrini Matteo
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
Methods Mol Biol. 2012;804:167-77. doi: 10.1007/978-1-61779-361-5_9.
Phylogenetic profiling involves the comparison of phylogenetic data across gene families. It is possible to construct phylogenetic trees, or related data structures, for specific gene families using a wide variety of tools and approaches. Phylogenetic profiling involves the comparison of this data to determine which families have correlated or coupled evolution. The underlying assumption is that in certain cases these couplings may allow us to infer that the two families are functionally related: that is their function in the cell is coupled. Although this technique can be applied to noncoding genes, it is more commonly used to assess the function of protein coding genes. Examples of proteins that are functionally related include subunits of protein complexes, or enzymes that perform consecutive steps along biochemical pathways. We hypothesize the deletion of one of the families from a genome would then indirectly affect the function of the other. Dozens of different implementations of the phylogenetic profiling technique have been developed over the past decade. These range from the first simple approaches that describe phylogenetic profiles as binary vectors to the most complex ones that attempt to model to the coevolution of protein families on a phylogenetic tree. We discuss a set of these implementations and present the software and databases that are available to perform phylogenetic profiling.
系统发育谱分析涉及跨基因家族比较系统发育数据。使用各种各样的工具和方法，为特定基因家族构建系统发育树或相关数据结构是可行的。系统发育谱分析涉及对这些数据进行比较，以确定哪些家族具有相关或耦合的进化。其基本假设是，在某些情况下，这些耦合可能使我们推断这两个家族在功能上相关：也就是说它们在细胞中的功能是耦合的。尽管这种技术可应用于非编码基因，但它更常用于评估蛋白质编码基因的功能。功能相关的蛋白质例子包括蛋白质复合物的亚基，或沿着生化途径执行连续步骤的酶。我们假设从基因组中删除其中一个家族会间接影响另一个家族的功能。在过去十年中，已经开发了几十种不同的系统发育谱分析技术实现。这些范围从最初将系统发育谱描述为二元向量的简单方法，到试图在系统发育树上模拟蛋白质家族协同进化的最复杂方法。我们讨论了其中的一组实现，并介绍了可用于执行系统发育谱分析的软件和数据库。
