Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s Disease
Objectives. This study aims to determine differentially expressed genes (DEGs) and long noncoding RNAs (lncRNAs) associated with Parkinson’s disease (PD) using a microarray. Methods. We downloaded the microarray data GSE6613 from the Gene Expression Omnibus, which included 105 samples. We selected 7...
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| Format: | Article |
| Language: | English |
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Wiley
2019-01-01
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| Series: | Parkinson's Disease |
| Online Access: | http://dx.doi.org/10.1155/2019/6078251 |
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| _version_ | 1849308925743071232 |
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| author | Lu-Mei Chi Li-Ping Wang Dan Jiao |
| author_facet | Lu-Mei Chi Li-Ping Wang Dan Jiao |
| author_sort | Lu-Mei Chi |
| collection | DOAJ |
| description | Objectives. This study aims to determine differentially expressed genes (DEGs) and long noncoding RNAs (lncRNAs) associated with Parkinson’s disease (PD) using a microarray. Methods. We downloaded the microarray data GSE6613 from the Gene Expression Omnibus, which included 105 samples. We selected 72 samples comprising 22 healthy control blood samples and 50 PD blood samples for further analysis. Later, we used Limma to screen DEGs and differentially expressed lncRNAs (DElncRNAs) and estimated their functions by the Gene Ontology (GO). Besides, the competing endogenous RNA (ceRNA) network, including microRNAs, lncRNAs, and mRNAs, was constructed to elucidate the regulatory mechanism. Furthermore, we performed the KEGG pathway enrichment with mRNAs in the ceRNA regulatory network and constructed a final network, including pathways, mRNAs, microRNAs, and lncRNAs. Results. Overall, we obtained 394 DEGs, including 207 upregulated DEGs and 187 downregulated DEGs, and 7 DElncRNAs, including 2 upregulated DElncRNAs and 5 downregulated DElncRNAs. Insulin-like growth factor-1 receptor (IGF1R) was considerably enriched in the endocytosis pathway. In the ceRNA regulation network, IGF1R was the target of hsa-miR-133b and lncRNAs of XIST, and PART1 could also be the target of hsa-miR-133b. While the upregulated DEGs were enriched in the GO terms of the cytoskeleton, cytoskeletal part, and microtubule cytoskeleton, the downregulated DEGs were enriched in the immune response. PRKACA was markedly enriched in numerous pathways, including the MAPK and insulin signaling pathways. Conclusions. IGF1R, PRKACA, and lncRNA-XIST could be potentially involved in PD, and these diverse molecular mechanisms could support the development of the similar treatment for PD. |
| format | Article |
| id | doaj-art-0b826d57562c4d69a111c2f608be7b2d |
| institution | Kabale University |
| issn | 2090-8083 2042-0080 |
| language | English |
| publishDate | 2019-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Parkinson's Disease |
| spelling | doaj-art-0b826d57562c4d69a111c2f608be7b2d2025-08-20T03:54:19ZengWileyParkinson's Disease2090-80832042-00802019-01-01201910.1155/2019/60782516078251Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s DiseaseLu-Mei Chi0Li-Ping Wang1Dan Jiao2Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun 130033, ChinaDepartment of Neurology, China-Japan Union Hospital of Jilin University, Changchun 130033, ChinaDepartment of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun 130033, ChinaObjectives. This study aims to determine differentially expressed genes (DEGs) and long noncoding RNAs (lncRNAs) associated with Parkinson’s disease (PD) using a microarray. Methods. We downloaded the microarray data GSE6613 from the Gene Expression Omnibus, which included 105 samples. We selected 72 samples comprising 22 healthy control blood samples and 50 PD blood samples for further analysis. Later, we used Limma to screen DEGs and differentially expressed lncRNAs (DElncRNAs) and estimated their functions by the Gene Ontology (GO). Besides, the competing endogenous RNA (ceRNA) network, including microRNAs, lncRNAs, and mRNAs, was constructed to elucidate the regulatory mechanism. Furthermore, we performed the KEGG pathway enrichment with mRNAs in the ceRNA regulatory network and constructed a final network, including pathways, mRNAs, microRNAs, and lncRNAs. Results. Overall, we obtained 394 DEGs, including 207 upregulated DEGs and 187 downregulated DEGs, and 7 DElncRNAs, including 2 upregulated DElncRNAs and 5 downregulated DElncRNAs. Insulin-like growth factor-1 receptor (IGF1R) was considerably enriched in the endocytosis pathway. In the ceRNA regulation network, IGF1R was the target of hsa-miR-133b and lncRNAs of XIST, and PART1 could also be the target of hsa-miR-133b. While the upregulated DEGs were enriched in the GO terms of the cytoskeleton, cytoskeletal part, and microtubule cytoskeleton, the downregulated DEGs were enriched in the immune response. PRKACA was markedly enriched in numerous pathways, including the MAPK and insulin signaling pathways. Conclusions. IGF1R, PRKACA, and lncRNA-XIST could be potentially involved in PD, and these diverse molecular mechanisms could support the development of the similar treatment for PD.http://dx.doi.org/10.1155/2019/6078251 |
| spellingShingle | Lu-Mei Chi Li-Ping Wang Dan Jiao Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s Disease Parkinson's Disease |
| title | Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s Disease |
| title_full | Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s Disease |
| title_fullStr | Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s Disease |
| title_full_unstemmed | Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s Disease |
| title_short | Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s Disease |
| title_sort | identification of differentially expressed genes and long noncoding rnas associated with parkinson s disease |
| url | http://dx.doi.org/10.1155/2019/6078251 |
| work_keys_str_mv | AT lumeichi identificationofdifferentiallyexpressedgenesandlongnoncodingrnasassociatedwithparkinsonsdisease AT lipingwang identificationofdifferentiallyexpressedgenesandlongnoncodingrnasassociatedwithparkinsonsdisease AT danjiao identificationofdifferentiallyexpressedgenesandlongnoncodingrnasassociatedwithparkinsonsdisease |