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NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies

The increasing number of OMICs studies demands bioinformatic tools that aid in the analysis of large sets of genes or proteins to understand their roles in the cell and establish functional networks and pathways. In the last decade, over-representation or enrichment tools have played a successful ro...

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Autores principales: Zúñiga-León, Eduardo, Carrasco-Navarro, Ulises, Fierro, Francisco
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6316660/
https://www.ncbi.nlm.nih.gov/pubmed/30477135
http://dx.doi.org/10.3390/genes9120569
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author Zúñiga-León, Eduardo
Carrasco-Navarro, Ulises
Fierro, Francisco
author_facet Zúñiga-León, Eduardo
Carrasco-Navarro, Ulises
Fierro, Francisco
author_sort Zúñiga-León, Eduardo
collection PubMed
description The increasing number of OMICs studies demands bioinformatic tools that aid in the analysis of large sets of genes or proteins to understand their roles in the cell and establish functional networks and pathways. In the last decade, over-representation or enrichment tools have played a successful role in the functional analysis of large gene/protein lists, which is evidenced by thousands of publications citing these tools. However, in most cases the results of these analyses are long lists of biological terms associated to proteins that are difficult to digest and interpret. Here we present NeVOmics, Network-based Visualization for Omics, a functional enrichment analysis tool that identifies statistically over-represented biological terms within a given gene/protein set. This tool provides a hypergeometric distribution test to calculate significantly enriched biological terms, and facilitates analysis on cluster distribution and relationship of proteins to processes and pathways. NeVOmics is adapted to use updated information from the two main annotation databases: Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG). NeVOmics compares favorably to other Gene Ontology and enrichment tools regarding coverage in the identification of biological terms. NeVOmics can also build different network-based graphical representations from the enrichment results, which makes it an integrative tool that greatly facilitates interpretation of results obtained by OMICs approaches. NeVOmics is freely accessible at https://github.com/bioinfproject/bioinfo/.
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spelling pubmed-63166602019-01-09 NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies Zúñiga-León, Eduardo Carrasco-Navarro, Ulises Fierro, Francisco Genes (Basel) Article The increasing number of OMICs studies demands bioinformatic tools that aid in the analysis of large sets of genes or proteins to understand their roles in the cell and establish functional networks and pathways. In the last decade, over-representation or enrichment tools have played a successful role in the functional analysis of large gene/protein lists, which is evidenced by thousands of publications citing these tools. However, in most cases the results of these analyses are long lists of biological terms associated to proteins that are difficult to digest and interpret. Here we present NeVOmics, Network-based Visualization for Omics, a functional enrichment analysis tool that identifies statistically over-represented biological terms within a given gene/protein set. This tool provides a hypergeometric distribution test to calculate significantly enriched biological terms, and facilitates analysis on cluster distribution and relationship of proteins to processes and pathways. NeVOmics is adapted to use updated information from the two main annotation databases: Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG). NeVOmics compares favorably to other Gene Ontology and enrichment tools regarding coverage in the identification of biological terms. NeVOmics can also build different network-based graphical representations from the enrichment results, which makes it an integrative tool that greatly facilitates interpretation of results obtained by OMICs approaches. NeVOmics is freely accessible at https://github.com/bioinfproject/bioinfo/. MDPI 2018-11-23 /pmc/articles/PMC6316660/ /pubmed/30477135 http://dx.doi.org/10.3390/genes9120569 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zúñiga-León, Eduardo
Carrasco-Navarro, Ulises
Fierro, Francisco
NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies
title NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies
title_full NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies
title_fullStr NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies
title_full_unstemmed NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies
title_short NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies
title_sort nevomics: an enrichment tool for gene ontology and functional network analysis and visualization of data from omics technologies
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6316660/
https://www.ncbi.nlm.nih.gov/pubmed/30477135
http://dx.doi.org/10.3390/genes9120569
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