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Gene Ontology Semantic Similarity Analysis Using GOSemSim

  • Guangchuang YuEmail author
Protocol
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Part of the Methods in Molecular Biology book series (MIMB, volume 2117)

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.

Key words

Semantic similarity GOSemSim Gene ontology Functional prediction Reproducible research 

Notes

Acknowledgments

I thank Drs. Yin Ge and Zhongtian Xu for providing useful feedback and helpful comments on the manuscript. This work was supported by Startup funds from Southern Medical University (G618289088).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Department of Bioinformatics, School of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina

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