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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

Box plots for miRNA and mRNA microarray datasets after normalization. (A) Box plot for miRNA microarray dataset after normalization; (B) box plot for mRNA microarray dataset after normalization. miRNA, microRNA.
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f1-mmr-12-04-4925: Box plots for miRNA and mRNA microarray datasets after normalization. (A) Box plot for miRNA microarray dataset after normalization; (B) box plot for mRNA microarray dataset after normalization. miRNA, microRNA.

Mentions: A total of 253 miRNAs and their associated 22,2215 genes were obtained based on their correlation between the miRNAs and associated genes of the original expression profile. Differentially expressed analyses of miRNA and mRNA were performed between cases and control by LIMMA package in R language and multiple comparisons using FDR and Benjamini and Hochberg after normalization (Fig. 1). A total of 850 DEGs and 9 miRNAs, including 3 up- and 6 downregulated miRNAs (Table I), were identified to be significantly expressed with thresholds of /log2 FC/>1 and FDR-corrected P<0.05.


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)

Box plots for miRNA and mRNA microarray datasets after normalization. (A) Box plot for miRNA microarray dataset after normalization; (B) box plot for mRNA microarray dataset after normalization. miRNA, microRNA.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1-mmr-12-04-4925: Box plots for miRNA and mRNA microarray datasets after normalization. (A) Box plot for miRNA microarray dataset after normalization; (B) box plot for mRNA microarray dataset after normalization. miRNA, microRNA.
Mentions: A total of 253 miRNAs and their associated 22,2215 genes were obtained based on their correlation between the miRNAs and associated genes of the original expression profile. Differentially expressed analyses of miRNA and mRNA were performed between cases and control by LIMMA package in R language and multiple comparisons using FDR and Benjamini and Hochberg after normalization (Fig. 1). A total of 850 DEGs and 9 miRNAs, including 3 up- and 6 downregulated miRNAs (Table I), were identified to be significantly expressed with thresholds of /log2 FC/>1 and FDR-corrected P<0.05.

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