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Microarray based analysis of gene regulation by microRNA in intervertebral disc degeneration.

Hu P, Feng B, Wang G, Ning B, Jia T - Mol Med Rep (2015)

Bottom Line: GSE 19943 and GSE 34095 datasets downloaded from Gene Expression Omnibus data were used to screen the differentially expressed genes (DEGs) in IDD.A total of 9 differentially expressed microRNAs, including 3 down‑ and 6 upregulated microRNAs and 850 DEGs were identified in tissue from patients with IDD.In conclusion, a comprehensive miRNA‑target gene regulatory network was constructed, which was found to be important in IDD progression.

View Article: PubMed Central - PubMed

Affiliation: Department of Orthopedics, Jinan Central Hospital of Shandong University, Jinan, Shandong 250012, P.R. China.

ABSTRACT
The present study aimed to explore the underlying mechanism of the development of intervertebral disc degeneration (IDD) by bioinformatics based on microarray datasets. GSE 19943 and GSE 34095 datasets downloaded from Gene Expression Omnibus data were used to screen the differentially expressed genes (DEGs) in IDD. The correlation between microRNAs and target genes was investigated using different algorithms. The underlying molecular mechanisms of the target genes were then explored using Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology function enrichment analysis. A total of 9 differentially expressed microRNAs, including 3 down‑ and 6 upregulated microRNAs and 850 DEGs were identified in tissue from patients with IDD. Two regulation networks of the target genes by microRNAs were constructed, including 33 upregulated microRNA‑target gene pairs and 4 downregulated microRNA‑target gene pairs. Certain target genes had been demonstrated to be involved in IDD progression via various pathways, including in the cell cycle and pathways in cancer. In addition, two important microRNAs (microRNA‑222 and microRNA‑589) were identified that were pivotal for the development of IDD, and their target genes, CDKNAB and SMAD4. In conclusion, a comprehensive miRNA‑target gene regulatory network was constructed, which was found to be important in IDD progression.

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Related in: MedlinePlus

Up- and downregulated miRNA-target genes network. (A) Upregulated miRNA-target genes network; (B) downregulated miRNA-target genes network. miRNA, microRNA.
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f2-mmr-12-04-4925: Up- and downregulated miRNA-target genes network. (A) Upregulated miRNA-target genes network; (B) downregulated miRNA-target genes network. miRNA, microRNA.

Mentions: To explore the regulation network for the target genes regulated by miRNAs, the correlation between proteins encoded by DEGs was identified by mapping both up- and downregulated DEGs to STRING. A total of 4 interaction pairs were constructed with a confidence score >0.4, including interaction relationships of SMAD family member 4 (SMAD4) and activin A receptor, type IB, WW domain containing adaptor with coiled-coil and bromodomain adjacent to zinc finger domain, 1B, BMI1 polycomb ring finger oncogene and cyclin-dependent kinase inhibitor 1B (CDKN1B), SMAD4 and CDKN1B. As shown in (Fig. 2), the interactions were visualized by Cytoscape. The network included 8 miRNA and 37 target DEGs, including miRNA-222 targeting the gene set of ataxin 1, BMI1, CDKN1B and defective in cullin neddylation 1, domain containing 4 and miRNA-589 targeting the gene set of F-box and WD repeat domain containing 2, G-rich RNA sequence binding factor 1, protein kinase N2 and SMAD4.


Microarray based analysis of gene regulation by microRNA in intervertebral disc degeneration.

Hu P, Feng B, Wang G, Ning B, Jia T - Mol Med Rep (2015)

Up- and downregulated miRNA-target genes network. (A) Upregulated miRNA-target genes network; (B) downregulated miRNA-target genes network. miRNA, microRNA.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4581765&req=5

f2-mmr-12-04-4925: Up- and downregulated miRNA-target genes network. (A) Upregulated miRNA-target genes network; (B) downregulated miRNA-target genes network. miRNA, microRNA.
Mentions: To explore the regulation network for the target genes regulated by miRNAs, the correlation between proteins encoded by DEGs was identified by mapping both up- and downregulated DEGs to STRING. A total of 4 interaction pairs were constructed with a confidence score >0.4, including interaction relationships of SMAD family member 4 (SMAD4) and activin A receptor, type IB, WW domain containing adaptor with coiled-coil and bromodomain adjacent to zinc finger domain, 1B, BMI1 polycomb ring finger oncogene and cyclin-dependent kinase inhibitor 1B (CDKN1B), SMAD4 and CDKN1B. As shown in (Fig. 2), the interactions were visualized by Cytoscape. The network included 8 miRNA and 37 target DEGs, including miRNA-222 targeting the gene set of ataxin 1, BMI1, CDKN1B and defective in cullin neddylation 1, domain containing 4 and miRNA-589 targeting the gene set of F-box and WD repeat domain containing 2, G-rich RNA sequence binding factor 1, protein kinase N2 and SMAD4.

Bottom Line: GSE 19943 and GSE 34095 datasets downloaded from Gene Expression Omnibus data were used to screen the differentially expressed genes (DEGs) in IDD.A total of 9 differentially expressed microRNAs, including 3 down‑ and 6 upregulated microRNAs and 850 DEGs were identified in tissue from patients with IDD.In conclusion, a comprehensive miRNA‑target gene regulatory network was constructed, which was found to be important in IDD progression.

View Article: PubMed Central - PubMed

Affiliation: Department of Orthopedics, Jinan Central Hospital of Shandong University, Jinan, Shandong 250012, P.R. China.

ABSTRACT
The present study aimed to explore the underlying mechanism of the development of intervertebral disc degeneration (IDD) by bioinformatics based on microarray datasets. GSE 19943 and GSE 34095 datasets downloaded from Gene Expression Omnibus data were used to screen the differentially expressed genes (DEGs) in IDD. The correlation between microRNAs and target genes was investigated using different algorithms. The underlying molecular mechanisms of the target genes were then explored using Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology function enrichment analysis. A total of 9 differentially expressed microRNAs, including 3 down‑ and 6 upregulated microRNAs and 850 DEGs were identified in tissue from patients with IDD. Two regulation networks of the target genes by microRNAs were constructed, including 33 upregulated microRNA‑target gene pairs and 4 downregulated microRNA‑target gene pairs. Certain target genes had been demonstrated to be involved in IDD progression via various pathways, including in the cell cycle and pathways in cancer. In addition, two important microRNAs (microRNA‑222 and microRNA‑589) were identified that were pivotal for the development of IDD, and their target genes, CDKNAB and SMAD4. In conclusion, a comprehensive miRNA‑target gene regulatory network was constructed, which was found to be important in IDD progression.

Show MeSH
Related in: MedlinePlus