GO 语义相似度分析：用于测量 GO 术语和基因产物之间语义相似性的 R 包。

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products.

机构信息

Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China.

出版信息

Bioinformatics. 2010 Apr 1;26(7):976-8. doi: 10.1093/bioinformatics/btq064. Epub 2010 Feb 23.

DOI:10.1093/bioinformatics/btq064

PMID:20179076

Abstract

SUMMARY

The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. Four information content (IC)- and a graph-based methods are implemented in the GOSemSim package, multiple species including human, rat, mouse, fly and yeast are also supported. The functions provided by the GOSemSim offer flexibility for applications, and can be easily integrated into high-throughput analysis pipelines.

AVAILABILITY

GOSemSim is released under the GNU General Public License within Bioconductor project, and freely available at http://bioconductor.org/packages/2.6/bioc/html/GOSemSim.html.

摘要

基因本体论 (GO) 注释的语义比较为计算基因和基因群之间的相似性提供了定量方法，已成为许多生物信息学分析方法的重要基础。GOSemSim 是一个用于计算 GO 术语、GO 术语集、基因产物和基因簇之间语义相似性的 R 包。该包实现了四种基于信息内容 (IC) 和基于图的方法，支持包括人类、大鼠、小鼠、果蝇和酵母在内的多个物种。GOSemSim 提供的功能为应用提供了灵活性，并且可以轻松集成到高通量分析管道中。