Thomas Paul D, Kejariwal Anish, Guo Nan, Mi Huaiyu, Campbell Michael J, Muruganujan Anushya, Lazareva-Ulitsky Betty
Evolutionary Systems Biology Group, SRI International 333 Ravenswood Ave., Menlo Park CA 94025, USA
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W645-50. doi: 10.1093/nar/gkl229.
The vast amount of protein sequence data now available, together with accumulating experimental knowledge of protein function, enables modeling of protein sequence and function evolution. The PANTHER database was designed to model evolutionary sequence-function relationships on a large scale. There are a number of applications for these data, and we have implemented web services that address three of them. The first is a protein classification service. Proteins can be classified, using only their amino acid sequences, to evolutionary groups at both the family and subfamily levels. Specific subfamilies, and often families, are further classified when possible according to their functions, including molecular function and the biological processes and pathways they participate in. The second application, then, is an expression data analysis service, where functional classification information can help find biological patterns in the data obtained from genome-wide experiments. The third application is a coding single-nucleotide polymorphism scoring service. In this case, information about evolutionarily related proteins is used to assess the likelihood of a deleterious effect on protein function arising from a single substitution at a specific amino acid position in the protein. All three web services are available at http://www.pantherdb.org/tools.
现有的大量蛋白质序列数据，连同不断积累的蛋白质功能实验知识，使得对蛋白质序列和功能进化进行建模成为可能。PANTHER数据库旨在大规模模拟进化序列-功能关系。这些数据有许多应用，我们已经实现了针对其中三项应用的网络服务。第一项是蛋白质分类服务。仅使用蛋白质的氨基酸序列，就可以将其分类到家族和亚家族水平的进化组中。特定的亚家族，而且在可能的情况下，家族还会根据其功能进一步分类，包括分子功能以及它们参与的生物过程和途径。第二项应用是表达数据分析服务，其中功能分类信息有助于在从全基因组实验获得的数据中发现生物学模式。第三项应用是编码单核苷酸多态性评分服务。在这种情况下，关于进化相关蛋白质的信息用于评估蛋白质中特定氨基酸位置的单个替换对蛋白质功能产生有害影响的可能性。所有这三项网络服务均可在http://www.pantherdb.org/tools上获取。
