Gene Ontology Semantic Similarity Analysis Using GOSemSim

Guangchuang Yu

doi:10.1007/978-1-0716-0301-7_11

Gene Ontology Semantic Similarity Analysis Using GOSemSim

Methods Mol Biol. 2020:2117:207-215. doi: 10.1007/978-1-0716-0301-7_11.

Author

Guangchuang Yu¹

Affiliation

¹ Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China. gcyu1@smu.edu.cn.

PMID: 31960380
DOI: 10.1007/978-1-0716-0301-7_11

Abstract

The GOSemSim package, an R-based tool within the Bioconductor project, offers several methods based on information content and graph structure for measuring semantic similarity among GO terms, gene products and gene clusters. In this chapter, I illustrate the use of GOSemSim on a list of regulators in preimplantation embryos. A step-by-step analysis was provided as well as instructions on interpretation and visualization of the results. GOSemSim is open-source and is available from https://www.bioconductor.org/packages/GOSemSim .

Keywords: Functional prediction; GOSemSim; Gene ontology; Reproducible research; Semantic similarity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
Gene Ontology*
Humans
Multigene Family
Semantics
Software