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Identification of crucial genes associated with rat traumatic spinal cord injury
The aim of the present study was to investigate the key genes associated with traumatic spinal cord injuries (TSCI). The dataset GSE52763 was downloaded from the Gene Expression Omnibus, for which lumbar spinal cord samples were obtained from rats at 1 and 3 weeks following contusive spinal cord inj...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
D.A. Spandidos
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5364992/ https://www.ncbi.nlm.nih.gov/pubmed/28260098 http://dx.doi.org/10.3892/mmr.2017.6267 |
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author | Yang, Zibin Lv, Qiao Wang, Zhengxiang Dong, Xiliang Yang, Rongxin Zhao, Wei |
author_facet | Yang, Zibin Lv, Qiao Wang, Zhengxiang Dong, Xiliang Yang, Rongxin Zhao, Wei |
author_sort | Yang, Zibin |
collection | PubMed |
description | The aim of the present study was to investigate the key genes associated with traumatic spinal cord injuries (TSCI). The dataset GSE52763 was downloaded from the Gene Expression Omnibus, for which lumbar spinal cord samples were obtained from rats at 1 and 3 weeks following contusive spinal cord injury and 1 week subsequent to a sham laminectomy, and used to identify differentially expressed genes (DEGs). Functional enrichment analysis, co-expression analysis and transcription factor (TF) identification were performed for DEGs common to the 1 and 3 week injury samples. In total, 234 upregulated and 51 downregulated DEGs were common to the 1 and 3 week injury samples. The upregulated DEGs were significantly enriched in Gene Ontology terms concerning immunity (e.g. Itgal and Ccl2) and certain pathways, including natural killer cell mediated cytotoxicity [e.g. Ras-related C3 botulinum toxin substrate 2 (Rac2) and TYRO protein tyrosine kinase binding protein (Tyrobp)]. The downregulated DEGs were highly enriched in female gonad development [e.g. progesterone receptor (Pgr)], and the steroid biosynthesis pathway. A total of 139 genes had co-expression associations and the majority of them were upregulated genes. The upregulated co-expressed genes were predominantly enriched in biological regulation, including TGFB induced factor homeobox 1 (Tgif1) and Rac2. The downregulated co-expressed genes were enriched in anatomical structure development (e.g. Dnm3). A total of 92 co-expressed genes composed the protein-protein interaction network. Additionally, 9 TFs (e.g. Pgr and Tgif1) were identified from the DEGs. It was hypothesized that the genes including Tgif1, Rac2, Tyrobp, and Pgr may be closely associated with TSCI. |
format | Online Article Text |
id | pubmed-5364992 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | D.A. Spandidos |
record_format | MEDLINE/PubMed |
spelling | pubmed-53649922017-05-15 Identification of crucial genes associated with rat traumatic spinal cord injury Yang, Zibin Lv, Qiao Wang, Zhengxiang Dong, Xiliang Yang, Rongxin Zhao, Wei Mol Med Rep Articles The aim of the present study was to investigate the key genes associated with traumatic spinal cord injuries (TSCI). The dataset GSE52763 was downloaded from the Gene Expression Omnibus, for which lumbar spinal cord samples were obtained from rats at 1 and 3 weeks following contusive spinal cord injury and 1 week subsequent to a sham laminectomy, and used to identify differentially expressed genes (DEGs). Functional enrichment analysis, co-expression analysis and transcription factor (TF) identification were performed for DEGs common to the 1 and 3 week injury samples. In total, 234 upregulated and 51 downregulated DEGs were common to the 1 and 3 week injury samples. The upregulated DEGs were significantly enriched in Gene Ontology terms concerning immunity (e.g. Itgal and Ccl2) and certain pathways, including natural killer cell mediated cytotoxicity [e.g. Ras-related C3 botulinum toxin substrate 2 (Rac2) and TYRO protein tyrosine kinase binding protein (Tyrobp)]. The downregulated DEGs were highly enriched in female gonad development [e.g. progesterone receptor (Pgr)], and the steroid biosynthesis pathway. A total of 139 genes had co-expression associations and the majority of them were upregulated genes. The upregulated co-expressed genes were predominantly enriched in biological regulation, including TGFB induced factor homeobox 1 (Tgif1) and Rac2. The downregulated co-expressed genes were enriched in anatomical structure development (e.g. Dnm3). A total of 92 co-expressed genes composed the protein-protein interaction network. Additionally, 9 TFs (e.g. Pgr and Tgif1) were identified from the DEGs. It was hypothesized that the genes including Tgif1, Rac2, Tyrobp, and Pgr may be closely associated with TSCI. D.A. Spandidos 2017-04 2017-03-01 /pmc/articles/PMC5364992/ /pubmed/28260098 http://dx.doi.org/10.3892/mmr.2017.6267 Text en Copyright: © Yang et al. This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. |
spellingShingle | Articles Yang, Zibin Lv, Qiao Wang, Zhengxiang Dong, Xiliang Yang, Rongxin Zhao, Wei Identification of crucial genes associated with rat traumatic spinal cord injury |
title | Identification of crucial genes associated with rat traumatic spinal cord injury |
title_full | Identification of crucial genes associated with rat traumatic spinal cord injury |
title_fullStr | Identification of crucial genes associated with rat traumatic spinal cord injury |
title_full_unstemmed | Identification of crucial genes associated with rat traumatic spinal cord injury |
title_short | Identification of crucial genes associated with rat traumatic spinal cord injury |
title_sort | identification of crucial genes associated with rat traumatic spinal cord injury |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5364992/ https://www.ncbi.nlm.nih.gov/pubmed/28260098 http://dx.doi.org/10.3892/mmr.2017.6267 |
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