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Gene Network Biological Validity Based on Gene-Gene Interaction Relevance

In recent years, gene networks have become one of the most useful tools for modeling biological processes. Many inference gene network algorithms have been developed as techniques for extracting knowledge from gene expression data. Ensuring the reliability of the inferred gene relationships is a cru...

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Detalles Bibliográficos
Autores principales: Gómez-Vela, Francisco, Díaz-Díaz, Norberto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4175387/
https://www.ncbi.nlm.nih.gov/pubmed/25295303
http://dx.doi.org/10.1155/2014/540679
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author Gómez-Vela, Francisco
Díaz-Díaz, Norberto
author_facet Gómez-Vela, Francisco
Díaz-Díaz, Norberto
author_sort Gómez-Vela, Francisco
collection PubMed
description In recent years, gene networks have become one of the most useful tools for modeling biological processes. Many inference gene network algorithms have been developed as techniques for extracting knowledge from gene expression data. Ensuring the reliability of the inferred gene relationships is a crucial task in any study in order to prove that the algorithms used are precise. Usually, this validation process can be carried out using prior biological knowledge. The metabolic pathways stored in KEGG are one of the most widely used knowledgeable sources for analyzing relationships between genes. This paper introduces a new methodology, GeneNetVal, to assess the biological validity of gene networks based on the relevance of the gene-gene interactions stored in KEGG metabolic pathways. Hence, a complete KEGG pathway conversion into a gene association network and a new matching distance based on gene-gene interaction relevance are proposed. The performance of GeneNetVal was established with three different experiments. Firstly, our proposal is tested in a comparative ROC analysis. Secondly, a randomness study is presented to show the behavior of GeneNetVal when the noise is increased in the input network. Finally, the ability of GeneNetVal to detect biological functionality of the network is shown.
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spelling pubmed-41753872014-10-07 Gene Network Biological Validity Based on Gene-Gene Interaction Relevance Gómez-Vela, Francisco Díaz-Díaz, Norberto ScientificWorldJournal Research Article In recent years, gene networks have become one of the most useful tools for modeling biological processes. Many inference gene network algorithms have been developed as techniques for extracting knowledge from gene expression data. Ensuring the reliability of the inferred gene relationships is a crucial task in any study in order to prove that the algorithms used are precise. Usually, this validation process can be carried out using prior biological knowledge. The metabolic pathways stored in KEGG are one of the most widely used knowledgeable sources for analyzing relationships between genes. This paper introduces a new methodology, GeneNetVal, to assess the biological validity of gene networks based on the relevance of the gene-gene interactions stored in KEGG metabolic pathways. Hence, a complete KEGG pathway conversion into a gene association network and a new matching distance based on gene-gene interaction relevance are proposed. The performance of GeneNetVal was established with three different experiments. Firstly, our proposal is tested in a comparative ROC analysis. Secondly, a randomness study is presented to show the behavior of GeneNetVal when the noise is increased in the input network. Finally, the ability of GeneNetVal to detect biological functionality of the network is shown. Hindawi Publishing Corporation 2014 2014-09-08 /pmc/articles/PMC4175387/ /pubmed/25295303 http://dx.doi.org/10.1155/2014/540679 Text en Copyright © 2014 F. Gómez-Vela and N. Díaz-Díaz. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Gómez-Vela, Francisco
Díaz-Díaz, Norberto
Gene Network Biological Validity Based on Gene-Gene Interaction Relevance
title Gene Network Biological Validity Based on Gene-Gene Interaction Relevance
title_full Gene Network Biological Validity Based on Gene-Gene Interaction Relevance
title_fullStr Gene Network Biological Validity Based on Gene-Gene Interaction Relevance
title_full_unstemmed Gene Network Biological Validity Based on Gene-Gene Interaction Relevance
title_short Gene Network Biological Validity Based on Gene-Gene Interaction Relevance
title_sort gene network biological validity based on gene-gene interaction relevance
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4175387/
https://www.ncbi.nlm.nih.gov/pubmed/25295303
http://dx.doi.org/10.1155/2014/540679
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