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Network analysis of single nucleotide polymorphisms in asthma
BACKGROUND: Asthma is a chronic inflammatory disease of the airways with a complex genetic background. In this study, we carried out a meta-analysis of single nucleotide polymorphisms (SNPs) thought to be associated with asthma. METHODS: The literature (PubMed) was searched for SNPs within genes rel...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Dove Medical Press
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047920/ https://www.ncbi.nlm.nih.gov/pubmed/21437052 http://dx.doi.org/10.2147/JAA.S14459 |
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author | Renkonen, Jutta Joenväärä, Sakari Parviainen, Ville Mattila, Pirkko Renkonen, Risto |
author_facet | Renkonen, Jutta Joenväärä, Sakari Parviainen, Ville Mattila, Pirkko Renkonen, Risto |
author_sort | Renkonen, Jutta |
collection | PubMed |
description | BACKGROUND: Asthma is a chronic inflammatory disease of the airways with a complex genetic background. In this study, we carried out a meta-analysis of single nucleotide polymorphisms (SNPs) thought to be associated with asthma. METHODS: The literature (PubMed) was searched for SNPs within genes relevant in asthma. The SNP-modified genes were converted to corresponding proteins, and their protein–protein interactions were searched from six different databases. This interaction network was analyzed using annotated vocabularies (ontologies), such as the Gene Ontology and Nature pathway interaction databases. RESULTS: In total, 127 genes with SNPs related to asthma were found in the literature. The corresponding proteins were then entered into a large protein–protein interaction network with the help of various databases. Ninety-six SNP-related proteins had more than one interacting protein each, and a network containing 309 proteins and 644 connections was generated. This network was significantly enriched with a gene ontology entitled “protein binding” and several of its daughter categories, including receptor binding and cytokine binding, when compared with the background human proteome. In the detailed analysis, the chemokine network, including eight proteins and 13 toll-like receptors, were shown to interact with each other. Of great interest are the nonsynonymous SNPs which code for an alternative amino acid sequence of proteins and, of the toll-like receptor network, TLR1, TLR4, TLR5, TLR6, TLR10, IL4R, and IL13 are among these. CONCLUSIONS: Protein binding, toll-like receptors, and chemokines dominated in the asthma-related protein interaction network. Systems level analysis of allergy-related mutations can provide new insights into the pathogenetic mechanisms of disease. |
format | Text |
id | pubmed-3047920 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Dove Medical Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-30479202011-03-23 Network analysis of single nucleotide polymorphisms in asthma Renkonen, Jutta Joenväärä, Sakari Parviainen, Ville Mattila, Pirkko Renkonen, Risto J Asthma Allergy Original Research BACKGROUND: Asthma is a chronic inflammatory disease of the airways with a complex genetic background. In this study, we carried out a meta-analysis of single nucleotide polymorphisms (SNPs) thought to be associated with asthma. METHODS: The literature (PubMed) was searched for SNPs within genes relevant in asthma. The SNP-modified genes were converted to corresponding proteins, and their protein–protein interactions were searched from six different databases. This interaction network was analyzed using annotated vocabularies (ontologies), such as the Gene Ontology and Nature pathway interaction databases. RESULTS: In total, 127 genes with SNPs related to asthma were found in the literature. The corresponding proteins were then entered into a large protein–protein interaction network with the help of various databases. Ninety-six SNP-related proteins had more than one interacting protein each, and a network containing 309 proteins and 644 connections was generated. This network was significantly enriched with a gene ontology entitled “protein binding” and several of its daughter categories, including receptor binding and cytokine binding, when compared with the background human proteome. In the detailed analysis, the chemokine network, including eight proteins and 13 toll-like receptors, were shown to interact with each other. Of great interest are the nonsynonymous SNPs which code for an alternative amino acid sequence of proteins and, of the toll-like receptor network, TLR1, TLR4, TLR5, TLR6, TLR10, IL4R, and IL13 are among these. CONCLUSIONS: Protein binding, toll-like receptors, and chemokines dominated in the asthma-related protein interaction network. Systems level analysis of allergy-related mutations can provide new insights into the pathogenetic mechanisms of disease. Dove Medical Press 2010-12-09 /pmc/articles/PMC3047920/ /pubmed/21437052 http://dx.doi.org/10.2147/JAA.S14459 Text en © 2010 Renkonen et al, publisher and licensee Dove Medical Press Ltd. This is an Open Access article which permits unrestricted noncommercial use, provided the original work is properly cited. |
spellingShingle | Original Research Renkonen, Jutta Joenväärä, Sakari Parviainen, Ville Mattila, Pirkko Renkonen, Risto Network analysis of single nucleotide polymorphisms in asthma |
title | Network analysis of single nucleotide polymorphisms in asthma |
title_full | Network analysis of single nucleotide polymorphisms in asthma |
title_fullStr | Network analysis of single nucleotide polymorphisms in asthma |
title_full_unstemmed | Network analysis of single nucleotide polymorphisms in asthma |
title_short | Network analysis of single nucleotide polymorphisms in asthma |
title_sort | network analysis of single nucleotide polymorphisms in asthma |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047920/ https://www.ncbi.nlm.nih.gov/pubmed/21437052 http://dx.doi.org/10.2147/JAA.S14459 |
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