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Identification of common coexpression modules based on quantitative network comparison
BACKGROUND: Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific interactions among genes. Therefore, identification of common coexpression net...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5998758/ https://www.ncbi.nlm.nih.gov/pubmed/29897320 http://dx.doi.org/10.1186/s12859-018-2193-3 |
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author | Jo, Yousang Kim, Sanghyeon Lee, Doheon |
author_facet | Jo, Yousang Kim, Sanghyeon Lee, Doheon |
author_sort | Jo, Yousang |
collection | PubMed |
description | BACKGROUND: Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific interactions among genes. Therefore, identification of common coexpression network or modules may reveal the molecular mechanism of complex disease or the relationship between biological processes. However, there has been no quantitative network comparison method for coexpression networks and we examined previous methods for other networks that cannot be applied to coexpression network. Therefore, we aimed to propose quantitative comparison methods for coexpression networks and to find common biological mechanisms between Huntington’s disease and brain aging by the new method. RESULTS: We proposed two similarity measures for quantitative comparison of coexpression networks. Then, we performed experiments using known coexpression networks. We showed the validity of two measures and evaluated threshold values for similar coexpression network pairs from experiments. Using these similarity measures and thresholds, we quantitatively measured the similarity between disease-specific and aging-related coexpression modules and found similar Huntington’s disease-aging coexpression module pairs. CONCLUSIONS: We identified similar Huntington’s disease-aging coexpression module pairs and found that these modules are related to brain development, cell death, and immune response. It suggests that up-regulated cell signalling related cell death and immune/ inflammation response may be the common molecular mechanisms in the pathophysiology of HD and normal brain aging in the frontal cortex. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2193-3) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5998758 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-59987582018-06-25 Identification of common coexpression modules based on quantitative network comparison Jo, Yousang Kim, Sanghyeon Lee, Doheon BMC Bioinformatics Research BACKGROUND: Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific interactions among genes. Therefore, identification of common coexpression network or modules may reveal the molecular mechanism of complex disease or the relationship between biological processes. However, there has been no quantitative network comparison method for coexpression networks and we examined previous methods for other networks that cannot be applied to coexpression network. Therefore, we aimed to propose quantitative comparison methods for coexpression networks and to find common biological mechanisms between Huntington’s disease and brain aging by the new method. RESULTS: We proposed two similarity measures for quantitative comparison of coexpression networks. Then, we performed experiments using known coexpression networks. We showed the validity of two measures and evaluated threshold values for similar coexpression network pairs from experiments. Using these similarity measures and thresholds, we quantitatively measured the similarity between disease-specific and aging-related coexpression modules and found similar Huntington’s disease-aging coexpression module pairs. CONCLUSIONS: We identified similar Huntington’s disease-aging coexpression module pairs and found that these modules are related to brain development, cell death, and immune response. It suggests that up-regulated cell signalling related cell death and immune/ inflammation response may be the common molecular mechanisms in the pathophysiology of HD and normal brain aging in the frontal cortex. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2193-3) contains supplementary material, which is available to authorized users. BioMed Central 2018-06-13 /pmc/articles/PMC5998758/ /pubmed/29897320 http://dx.doi.org/10.1186/s12859-018-2193-3 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Jo, Yousang Kim, Sanghyeon Lee, Doheon Identification of common coexpression modules based on quantitative network comparison |
title | Identification of common coexpression modules based on quantitative network comparison |
title_full | Identification of common coexpression modules based on quantitative network comparison |
title_fullStr | Identification of common coexpression modules based on quantitative network comparison |
title_full_unstemmed | Identification of common coexpression modules based on quantitative network comparison |
title_short | Identification of common coexpression modules based on quantitative network comparison |
title_sort | identification of common coexpression modules based on quantitative network comparison |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5998758/ https://www.ncbi.nlm.nih.gov/pubmed/29897320 http://dx.doi.org/10.1186/s12859-018-2193-3 |
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