Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany.
Nucleic Acids Res. 2010 Jan;38(Database issue):D244-8. doi: 10.1093/nar/gkp979. Epub 2009 Nov 18.
Quantifying the functional similarity of genes and their products based on Gene Ontology annotation is an important tool for diverse applications like the analysis of gene expression data, the prediction and validation of protein functions and interactions, and the prioritization of disease genes. The Functional Similarity Matrix (FunSimMat, http://www.funsimmat.de) is a comprehensive database providing various precomputed functional similarity values for proteins in UniProtKB and for protein families in Pfam and SMART. With this update, we significantly increase the coverage of FunSimMat by adding data from the Gene Ontology Annotation project as well as new functional similarity measures. The applicability of the database is greatly extended by the implementation of a new Gene Ontology-based method for disease gene prioritization. Two new visualization tools allow an interactive analysis of the functional relationships between proteins or protein families. This is enhanced further by the introduction of an automatically derived hierarchy of annotation classes. Additional changes include a revised user front-end and a new RESTlike interface for improving the user-friendliness and online accessibility of FunSimMat.
基于基因本体论（GO）注释来量化基因及其产物的功能相似性是各种应用的重要工具，例如基因表达数据分析、蛋白质功能和相互作用的预测和验证，以及疾病基因的优先级排序。功能相似性矩阵（FunSimMat，http://www.funsimmat.de）是一个综合数据库，为 UniProtKB 中的蛋白质和 Pfam 和 SMART 中的蛋白质家族提供了各种预先计算的功能相似性值。通过此次更新，我们通过添加来自基因本体论注释项目的数据以及新的功能相似性度量标准，大大增加了 FunSimMat 的覆盖范围。通过实现一种新的基于基因本体论的疾病基因优先级排序方法，极大地扩展了数据库的适用性。两个新的可视化工具允许对蛋白质或蛋白质家族之间的功能关系进行交互式分析。通过引入自动衍生的注释类层次结构，进一步增强了这种分析能力。其他更改包括修订的用户前端和新的类似 REST 的接口，以提高 FunSimMat 的用户友好性和在线可访问性。
