Meta-Analysis of Gene Expression and Identification of Biological Regulatory Mechanisms in Alzheimer's Disease
Alzheimer's disease (AD), also known as senile dementia, is a progressive neurodegenerative disease. The etiology and pathogenesis of AD have not yet been elucidated. We examined common differentially expressed genes (DEGs) from different AD tissue microarray datasets by meta-analysis and scree...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-07-01
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| Series: | Frontiers in Neuroscience |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fnins.2019.00633/full |
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| author | Lining Su Sufen Chen Chenqing Zheng Huiping Wei Xiaoqing Song |
| author_facet | Lining Su Sufen Chen Chenqing Zheng Huiping Wei Xiaoqing Song |
| author_sort | Lining Su |
| collection | DOAJ |
| description | Alzheimer's disease (AD), also known as senile dementia, is a progressive neurodegenerative disease. The etiology and pathogenesis of AD have not yet been elucidated. We examined common differentially expressed genes (DEGs) from different AD tissue microarray datasets by meta-analysis and screened the AD-associated genes from the common DEGs using GCBI. Then we studied the gene expression network using the STRING database and identified the hub genes using Cytoscape. Furthermore, we analyzed the microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and single nucleotide polymorphisms (SNPs) associated with the AD-associated genes, and then identified feed-forward loops. Finally, we performed SNP analysis of the AD-associated genes. Our results identified 207 common DEGs, of which 57 have previously been reported to be associated with AD. The common DEG expression network identified eight hub genes, all of which were previously known to be associated with AD. Further study of the regulatory miRNAs associated with the AD-associated genes and other genes specific to neurodegenerative diseases revealed 65 AD-associated miRNAs. Analysis of the miRNA associated transcription factor-miRNA-gene-gene associated TF (mTF-miRNA-gene-gTF) network around the AD-associated genes revealed 131 feed-forward loops (FFLs). Among them, one important FFL was found between the gene SERPINA3, hsa-miR-27a, and the transcription factor MYC. Furthermore, SNP analysis of the AD-associated genes identified 173 SNPs, and also found a role in AD for miRNAs specific to other neurodegenerative diseases, including hsa-miR-34c, hsa-miR-212, hsa-miR-34a, and hsa-miR-7. The regulatory network constructed in this study describes the mechanism of cell regulation in AD, in which miRNAs and lncRNAs can be considered AD regulatory factors. |
| first_indexed | 2024-12-22T15:08:11Z |
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| id | doaj.art-acc27c944ab3425280dd5643dc18e1e0 |
| institution | Directory Open Access Journal |
| issn | 1662-453X |
| language | English |
| last_indexed | 2024-12-22T15:08:11Z |
| publishDate | 2019-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroscience |
| spelling | doaj.art-acc27c944ab3425280dd5643dc18e1e02022-12-21T18:21:56ZengFrontiers Media S.A.Frontiers in Neuroscience1662-453X2019-07-011310.3389/fnins.2019.00633454652Meta-Analysis of Gene Expression and Identification of Biological Regulatory Mechanisms in Alzheimer's DiseaseLining Su0Sufen Chen1Chenqing Zheng2Huiping Wei3Xiaoqing Song4Department of Basic Medicine, Hebei North University, Zhangjiakou, ChinaInstitute of Educational Science, Zhangjiakou, ChinaShenzhen RealOmics (Biotech) Co., Ltd., Shenzhen, ChinaDepartment of Basic Medicine, Hebei North University, Zhangjiakou, ChinaDepartment of Basic Medicine, Hebei North University, Zhangjiakou, ChinaAlzheimer's disease (AD), also known as senile dementia, is a progressive neurodegenerative disease. The etiology and pathogenesis of AD have not yet been elucidated. We examined common differentially expressed genes (DEGs) from different AD tissue microarray datasets by meta-analysis and screened the AD-associated genes from the common DEGs using GCBI. Then we studied the gene expression network using the STRING database and identified the hub genes using Cytoscape. Furthermore, we analyzed the microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and single nucleotide polymorphisms (SNPs) associated with the AD-associated genes, and then identified feed-forward loops. Finally, we performed SNP analysis of the AD-associated genes. Our results identified 207 common DEGs, of which 57 have previously been reported to be associated with AD. The common DEG expression network identified eight hub genes, all of which were previously known to be associated with AD. Further study of the regulatory miRNAs associated with the AD-associated genes and other genes specific to neurodegenerative diseases revealed 65 AD-associated miRNAs. Analysis of the miRNA associated transcription factor-miRNA-gene-gene associated TF (mTF-miRNA-gene-gTF) network around the AD-associated genes revealed 131 feed-forward loops (FFLs). Among them, one important FFL was found between the gene SERPINA3, hsa-miR-27a, and the transcription factor MYC. Furthermore, SNP analysis of the AD-associated genes identified 173 SNPs, and also found a role in AD for miRNAs specific to other neurodegenerative diseases, including hsa-miR-34c, hsa-miR-212, hsa-miR-34a, and hsa-miR-7. The regulatory network constructed in this study describes the mechanism of cell regulation in AD, in which miRNAs and lncRNAs can be considered AD regulatory factors.https://www.frontiersin.org/article/10.3389/fnins.2019.00633/fullAlzheimer's diseaselong non-coding RNAmicroRNAsingle nucleotide polymorphismsnetworkmeta-analysis |
| spellingShingle | Lining Su Sufen Chen Chenqing Zheng Huiping Wei Xiaoqing Song Meta-Analysis of Gene Expression and Identification of Biological Regulatory Mechanisms in Alzheimer's Disease Frontiers in Neuroscience Alzheimer's disease long non-coding RNA microRNA single nucleotide polymorphisms network meta-analysis |
| title | Meta-Analysis of Gene Expression and Identification of Biological Regulatory Mechanisms in Alzheimer's Disease |
| title_full | Meta-Analysis of Gene Expression and Identification of Biological Regulatory Mechanisms in Alzheimer's Disease |
| title_fullStr | Meta-Analysis of Gene Expression and Identification of Biological Regulatory Mechanisms in Alzheimer's Disease |
| title_full_unstemmed | Meta-Analysis of Gene Expression and Identification of Biological Regulatory Mechanisms in Alzheimer's Disease |
| title_short | Meta-Analysis of Gene Expression and Identification of Biological Regulatory Mechanisms in Alzheimer's Disease |
| title_sort | meta analysis of gene expression and identification of biological regulatory mechanisms in alzheimer s disease |
| topic | Alzheimer's disease long non-coding RNA microRNA single nucleotide polymorphisms network meta-analysis |
| url | https://www.frontiersin.org/article/10.3389/fnins.2019.00633/full |
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