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MicroRNA expression data analysis to identify key miRNAs associated with Alzheimer's disease.
J Gene Med. 2018 06; 20(6):e3014.JG

Abstract

BACKGROUND

MicroRNAs (miRNAs) have become increasingly prevalent as a result of the association of their deregulation with neurodegenerative disorders, especially Alzheimer's disease (AD). However, the association between miRNAs and AD remains unclear.

METHODS

In the present study, Nine representative miRNA datasets were selected for the identification of the critical miRNAs by analyzing the overlapping relationships among them. TargetScan software (http://www.targetscan.org) was used to predict the target genes of these miRNAs. In addition, the Database for Annotation Visualization and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov) and TfactS (http://www.tfacts.org) datasets were used for combined analysis of functional enrichment and transcription factor (TF) analysis.

RESULTS

Thirteen key miRNAs were identified, of which four were significantly up-regulated (hsa-miR-101,hsa-miR-155, has-miR-34a, has-miR-9) and eight were found to be significantly down-regulated (hsa-let-7d-5p, hsa-let-7 g-5p, hsa-miR-15b, has-miR-191-5p, hsa-miR-125b, has-miR-26b-5p, hsa-miR-29b, hsa-miR-342-3p). The functional enrichment analysis indicated that up-regulated signature miRNA targets were associated with transcription from the RNA polymerase II promoter process and the chemical synaptic transmission process. Down-regulated signature miRNA targets were mostly enriched with respect to positive regulation of transcription from the RNA polymerase II promoter process, p53 signaling, and microRNAs in cancer pathways. TF analysis showed that 87 TFs were influenced by the up-regulated miRNAs, and 134 TFs were influenced by the down-regulated miRNAs. In total, 70 (45.5%) TFs were affected by both up-regulated and down-regulated miRNAs.

CONCLUSIONS

In summary, 13 key miRNAs were found to have a vital function in the pathological progress of AD, as well as the target genes and TFs of these miRNAs. The potential functions of these miRNAs as diagnostic and therapeutic targets of the AD are revealed by the present study.

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Publisher Full Text (DOI)

Authors+Show Affiliations

Chen J
Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.
Qi Y
Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.
Liu CF
Department of Rehabilitation, The Central Hospital of Xianning, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning, Hubei, China.
Lu JM
Department of Neurology, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China.
Shi J
Geriatric Department, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
Shi Y
Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.

MeSH

Alzheimer DiseaseComputational BiologyDatabases, GeneticGene Expression ProfilingHumansMicroRNAsTranscription Factors

Pub Type(s)

Journal Article

Language

eng

PubMed ID

29543360

Citation

Chen, Jing, et al. "MicroRNA Expression Data Analysis to Identify Key miRNAs Associated With Alzheimer's Disease." The Journal of Gene Medicine, vol. 20, no. 6, 2018, pp. e3014.
Chen J, Qi Y, Liu CF, et al. MicroRNA expression data analysis to identify key miRNAs associated with Alzheimer's disease. J Gene Med. 2018;20(6):e3014.
Chen, J., Qi, Y., Liu, C. F., Lu, J. M., Shi, J., & Shi, Y. (2018). MicroRNA expression data analysis to identify key miRNAs associated with Alzheimer's disease. The Journal of Gene Medicine, 20(6), e3014. https://doi.org/10.1002/jgm.3014
Chen J, et al. MicroRNA Expression Data Analysis to Identify Key miRNAs Associated With Alzheimer's Disease. J Gene Med. 2018;20(6):e3014. PubMed PMID: 29543360.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - MicroRNA expression data analysis to identify key miRNAs associated with Alzheimer's disease. AU - Chen,Jing, AU - Qi,Yan, AU - Liu,Cui-Fang, AU - Lu,Jing-Min, AU - Shi,Jing, AU - Shi,Yan, Y1 - 2018/05/21/ PY - 2017/12/13/received PY - 2018/03/06/revised PY - 2018/03/07/accepted PY - 2018/3/16/pubmed PY - 2019/9/26/medline PY - 2018/3/16/entrez KW - Alzheimer's disease KW - gene set enrichment analysis KW - miRNAs KW - transcription factor analysis SP - e3014 EP - e3014 JF - The journal of gene medicine JO - J Gene Med VL - 20 IS - 6 N2 - BACKGROUND: MicroRNAs (miRNAs) have become increasingly prevalent as a result of the association of their deregulation with neurodegenerative disorders, especially Alzheimer's disease (AD). However, the association between miRNAs and AD remains unclear. METHODS: In the present study, Nine representative miRNA datasets were selected for the identification of the critical miRNAs by analyzing the overlapping relationships among them. TargetScan software (http://www.targetscan.org) was used to predict the target genes of these miRNAs. In addition, the Database for Annotation Visualization and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov) and TfactS (http://www.tfacts.org) datasets were used for combined analysis of functional enrichment and transcription factor (TF) analysis. RESULTS: Thirteen key miRNAs were identified, of which four were significantly up-regulated (hsa-miR-101,hsa-miR-155, has-miR-34a, has-miR-9) and eight were found to be significantly down-regulated (hsa-let-7d-5p, hsa-let-7 g-5p, hsa-miR-15b, has-miR-191-5p, hsa-miR-125b, has-miR-26b-5p, hsa-miR-29b, hsa-miR-342-3p). The functional enrichment analysis indicated that up-regulated signature miRNA targets were associated with transcription from the RNA polymerase II promoter process and the chemical synaptic transmission process. Down-regulated signature miRNA targets were mostly enriched with respect to positive regulation of transcription from the RNA polymerase II promoter process, p53 signaling, and microRNAs in cancer pathways. TF analysis showed that 87 TFs were influenced by the up-regulated miRNAs, and 134 TFs were influenced by the down-regulated miRNAs. In total, 70 (45.5%) TFs were affected by both up-regulated and down-regulated miRNAs. CONCLUSIONS: In summary, 13 key miRNAs were found to have a vital function in the pathological progress of AD, as well as the target genes and TFs of these miRNAs. The potential functions of these miRNAs as diagnostic and therapeutic targets of the AD are revealed by the present study. SN - 1521-2254 UR - https://www.unboundmedicine.com/medline/citation/29543360/MicroRNA_expression_data_analysis_to_identify_key_miRNAs_associated_with_Alzheimer's_disease_ DB - PRIME DP - Unbound Medicine ER -