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Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs
BACKGROUND: Differential coexpression analysis (DCEA) is increasingly used for investigating the global transcriptional mechanisms underlying phenotypic changes. Current DCEA methods mostly adopt a gene connectivity-based strategy to estimate differential coexpression, which is characterized by comp...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199761/ https://www.ncbi.nlm.nih.gov/pubmed/21806838 http://dx.doi.org/10.1186/1471-2105-12-315 |
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author | Yu, Hui Liu, Bao-Hong Ye, Zhi-Qiang Li, Chun Li, Yi-Xue Li, Yuan-Yuan |
author_facet | Yu, Hui Liu, Bao-Hong Ye, Zhi-Qiang Li, Chun Li, Yi-Xue Li, Yuan-Yuan |
author_sort | Yu, Hui |
collection | PubMed |
description | BACKGROUND: Differential coexpression analysis (DCEA) is increasingly used for investigating the global transcriptional mechanisms underlying phenotypic changes. Current DCEA methods mostly adopt a gene connectivity-based strategy to estimate differential coexpression, which is characterized by comparing the numbers of gene neighbors in different coexpression networks. Although it simplifies the calculation, this strategy mixes up the identities of different coexpression neighbors of a gene, and fails to differentiate significant differential coexpression changes from those trivial ones. Especially, the correlation-reversal is easily missed although it probably indicates remarkable biological significance. RESULTS: We developed two link-based quantitative methods, DCp and DCe, to identify differentially coexpressed genes and gene pairs (links). Bearing the uniqueness of exploiting the quantitative coexpression change of each gene pair in the coexpression networks, both methods proved to be superior to currently popular methods in simulation studies. Re-mining of a publicly available type 2 diabetes (T2D) expression dataset from the perspective of differential coexpression analysis led to additional discoveries than those from differential expression analysis. CONCLUSIONS: This work pointed out the critical weakness of current popular DCEA methods, and proposed two link-based DCEA algorithms that will make contribution to the development of DCEA and help extend it to a broader spectrum. |
format | Online Article Text |
id | pubmed-3199761 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-31997612011-10-24 Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs Yu, Hui Liu, Bao-Hong Ye, Zhi-Qiang Li, Chun Li, Yi-Xue Li, Yuan-Yuan BMC Bioinformatics Methodology Article BACKGROUND: Differential coexpression analysis (DCEA) is increasingly used for investigating the global transcriptional mechanisms underlying phenotypic changes. Current DCEA methods mostly adopt a gene connectivity-based strategy to estimate differential coexpression, which is characterized by comparing the numbers of gene neighbors in different coexpression networks. Although it simplifies the calculation, this strategy mixes up the identities of different coexpression neighbors of a gene, and fails to differentiate significant differential coexpression changes from those trivial ones. Especially, the correlation-reversal is easily missed although it probably indicates remarkable biological significance. RESULTS: We developed two link-based quantitative methods, DCp and DCe, to identify differentially coexpressed genes and gene pairs (links). Bearing the uniqueness of exploiting the quantitative coexpression change of each gene pair in the coexpression networks, both methods proved to be superior to currently popular methods in simulation studies. Re-mining of a publicly available type 2 diabetes (T2D) expression dataset from the perspective of differential coexpression analysis led to additional discoveries than those from differential expression analysis. CONCLUSIONS: This work pointed out the critical weakness of current popular DCEA methods, and proposed two link-based DCEA algorithms that will make contribution to the development of DCEA and help extend it to a broader spectrum. BioMed Central 2011-08-02 /pmc/articles/PMC3199761/ /pubmed/21806838 http://dx.doi.org/10.1186/1471-2105-12-315 Text en Copyright ©2011 Yu et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Yu, Hui Liu, Bao-Hong Ye, Zhi-Qiang Li, Chun Li, Yi-Xue Li, Yuan-Yuan Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs |
title | Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs |
title_full | Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs |
title_fullStr | Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs |
title_full_unstemmed | Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs |
title_short | Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs |
title_sort | link-based quantitative methods to identify differentially coexpressed genes and gene pairs |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199761/ https://www.ncbi.nlm.nih.gov/pubmed/21806838 http://dx.doi.org/10.1186/1471-2105-12-315 |
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