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Co-expression network analysis revealing the key lncRNAs in diabetic foot ulcers
INTRODUCTION: Diabetic foot ulcers (DFUs) are the most common foot injuries leading to lower extremity amputation in diabetic patients. Recent studies showed that long non-coding RNAs (lncRNAs) played important roles in diverse biological processes. In this study, we focused on identifying different...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Termedia Publishing House
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764308/ https://www.ncbi.nlm.nih.gov/pubmed/31572456 http://dx.doi.org/10.5114/aoms.2019.84699 |
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author | Yu, Pijun Guo, Jian Li, Junjie Chen, Wei Zhao, Tianlan |
author_facet | Yu, Pijun Guo, Jian Li, Junjie Chen, Wei Zhao, Tianlan |
author_sort | Yu, Pijun |
collection | PubMed |
description | INTRODUCTION: Diabetic foot ulcers (DFUs) are the most common foot injuries leading to lower extremity amputation in diabetic patients. Recent studies showed that long non-coding RNAs (lncRNAs) played important roles in diverse biological processes. In this study, we focused on identifying differentially expressed long non-coding RNAs (lncRNAs) in DFU. MATERIAL AND METHODS: Real-time PCR assay was performed to validate the expression pattern of lncRNAs in DFU. Moreover, co-expression networks were also constructed to identify hub lncRNAs in DFU. Specifically, gene ontology (GO) analysis was first performed to evaluate the potential roles of differentially expressed genes (DEGs) and lncRNAs in DFU. RESULTS: In the present study, we identified 58 up-regulated lncRNAs and 42 down-regulated lncRNAs in DFU samples compared to non-diabetic foot skin samples by analyzing the GSE68186 dataset. Four lncRNAs (FLJ30679, LINC01193, LINC00692, and LINC00641) were observed to be up-regulated in DFU. Furthermore, we found that the down-regulated lncRNA-mediated co-expression network contained 42 lncRNAs and 700 DEGs and the up-regulated lncRNA mediated co-expression network contained 58 lncRNAs and 688 DEGs. CONCLUSIONS: Bioinformatics analysis showed that differentially expressed lncRNAs were involved in regulating the ERK1 and ERK2 cascade, secondary alcohol biosynthetic process, centrosome duplication and DNA repair. These results suggested the potential prognostic value of lncRNAs in DFU. |
format | Online Article Text |
id | pubmed-6764308 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Termedia Publishing House |
record_format | MEDLINE/PubMed |
spelling | pubmed-67643082019-09-30 Co-expression network analysis revealing the key lncRNAs in diabetic foot ulcers Yu, Pijun Guo, Jian Li, Junjie Chen, Wei Zhao, Tianlan Arch Med Sci Basic Research INTRODUCTION: Diabetic foot ulcers (DFUs) are the most common foot injuries leading to lower extremity amputation in diabetic patients. Recent studies showed that long non-coding RNAs (lncRNAs) played important roles in diverse biological processes. In this study, we focused on identifying differentially expressed long non-coding RNAs (lncRNAs) in DFU. MATERIAL AND METHODS: Real-time PCR assay was performed to validate the expression pattern of lncRNAs in DFU. Moreover, co-expression networks were also constructed to identify hub lncRNAs in DFU. Specifically, gene ontology (GO) analysis was first performed to evaluate the potential roles of differentially expressed genes (DEGs) and lncRNAs in DFU. RESULTS: In the present study, we identified 58 up-regulated lncRNAs and 42 down-regulated lncRNAs in DFU samples compared to non-diabetic foot skin samples by analyzing the GSE68186 dataset. Four lncRNAs (FLJ30679, LINC01193, LINC00692, and LINC00641) were observed to be up-regulated in DFU. Furthermore, we found that the down-regulated lncRNA-mediated co-expression network contained 42 lncRNAs and 700 DEGs and the up-regulated lncRNA mediated co-expression network contained 58 lncRNAs and 688 DEGs. CONCLUSIONS: Bioinformatics analysis showed that differentially expressed lncRNAs were involved in regulating the ERK1 and ERK2 cascade, secondary alcohol biosynthetic process, centrosome duplication and DNA repair. These results suggested the potential prognostic value of lncRNAs in DFU. Termedia Publishing House 2019-05-05 2019-09 /pmc/articles/PMC6764308/ /pubmed/31572456 http://dx.doi.org/10.5114/aoms.2019.84699 Text en Copyright: © 2019 Termedia & Banach http://creativecommons.org/licenses/by-nc-sa/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License, allowing third parties to copy and redistribute the material in any medium or format and to remix, transform, and build upon the material, provided the original work is properly cited and states its license. |
spellingShingle | Basic Research Yu, Pijun Guo, Jian Li, Junjie Chen, Wei Zhao, Tianlan Co-expression network analysis revealing the key lncRNAs in diabetic foot ulcers |
title | Co-expression network analysis revealing the key lncRNAs in diabetic foot ulcers |
title_full | Co-expression network analysis revealing the key lncRNAs in diabetic foot ulcers |
title_fullStr | Co-expression network analysis revealing the key lncRNAs in diabetic foot ulcers |
title_full_unstemmed | Co-expression network analysis revealing the key lncRNAs in diabetic foot ulcers |
title_short | Co-expression network analysis revealing the key lncRNAs in diabetic foot ulcers |
title_sort | co-expression network analysis revealing the key lncrnas in diabetic foot ulcers |
topic | Basic Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764308/ https://www.ncbi.nlm.nih.gov/pubmed/31572456 http://dx.doi.org/10.5114/aoms.2019.84699 |
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