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Computing and Visualizing Gene Function Similarity and Coherence with NaviGO

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1807)

Abstract

Gene ontology (GO) is a controlled vocabulary of gene functions across all species, which is widely used for functional analyses of individual genes and large-scale proteomic studies. NaviGO is a webserver for visualizing and quantifying the relationship and similarity of GO annotations. Here, we walk through functionality of the NaviGO webserver (http://kiharalab.org/web/navigo/) using an example input and explain what can be learned from analysis results. NaviGO has four main functions, accessed from each page of the webserver: “GO Parents,” “GO Set”, “GO Enrichment”, and “Protein Set.” For a given list of GO terms, the “GO Parents” tab visualizes the hierarchical relationship of GO terms, and the “GO Set” tab calculates six functional similarity and association scores and presents results in a network and a multidimensional scaling plot. For a set of proteins and their associated GO terms, the “GO Enrichment” tab calculates protein GO functional enrichment, while the “Protein Set” tab calculates functional association between proteins. The NaviGO source code can be also downloaded and used locally or integrated into other software pipelines.

Key words

NaviGO Gene ontology Functional similarity Visualization Quantification Function enrichment analysis GO association score Protein functional association score Proteomic analysis 
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Notes

Acknowledgments

We thank Charles Christoffer for proofreading the manuscript. This work was partly supported by the National Institute of General Medical Sciences of the NIH (R01GM123055) and the National Science Foundation (DBI1262189, IOS1127027, DMS1614777).

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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Biological SciencePurdue UniversityWest LafayetteUSA
  2. 2.Department of Computer SciencePurdue UniversityWest LafayetteUSA

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