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BMC Bioinformatics. 2017 Mar 20;18(1):177. doi: 10.1186/s12859-017-1600-5.

NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.

Author information

1
Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.
2
Department of Biological Science, Purdue University, West Lafayette, IN, 47907, USA.
3
Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, 55905, USA.
4
Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA. dkihara@purdue.edu.
5
Department of Biological Science, Purdue University, West Lafayette, IN, 47907, USA. dkihara@purdue.edu.

Abstract

BACKGROUND:

The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were developed and improved to enable fast and automatic function annotation. With the well-defined structure and manual curation, Gene Ontology (GO) is the most frequently used vocabulary for representing gene functions. To understand relationship and similarity between GO annotations of genes, it is important to have a convenient pipeline that quantifies and visualizes the GO function analyses in a systematic fashion.

RESULTS:

NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes. Similarity of GO terms and gene functions is quantified with six different scores including protein-protein interaction and context based association scores we have developed in our previous works. Interactive navigation of the GO function space provides intuitive and effective real-time visualization of functional groupings of GO terms and genes as well as statistical analysis of enriched functions.

CONCLUSIONS:

We developed NaviGO, which visualizes and analyses functional similarity and associations of GO terms and genes. The NaviGO webserver is freely available at: http://kiharalab.org/web/navigo .

KEYWORDS:

Function similarity; GO; GO annotation; GO association score; GO directed acyclic graph; GO parental terms; Gene function; Gene function prediction; Gene ontology; Ontology; function enrichment analysis

PMID:
28320317
PMCID:
PMC5359872
DOI:
10.1186/s12859-017-1600-5
[Indexed for MEDLINE]
Free PMC Article

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