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Bioinformatics analysis to identify the differentially expressed genes of glaucoma.

Yan X, Yuan F, Chen X, Dong C - Mol Med Rep (2015)

Bottom Line: In addition, the DEGs were found to be associated with several functions, including response to wounding, extracellular region part and calcium ion binding.The most significantly enriched pathways were complement and coagulation cascades, arrhythmogenic right ventricular cardiomyopathy and extracellular matrix (ECM)‑receptor interaction.Additionally, 37 and 31 GO terms were identified to be enriched in the two DEGs of the networks prior to and subsequent to summation, respectively.

View Article: PubMed Central - PubMed

Affiliation: Department of Ophthalmology, Pudong District Gongli Hospital, Shanghai 200135, P.R. China.

ABSTRACT
The aim of the present study was to screen the differentially expressed genes (DEGs) associated with glaucoma and investigate the changing patterns of the expression of these genes. The GSE2378 gene microarray data of glaucoma was downloaded from the Gene Expression Omnibus database, which included seven normal samples and eight glaucoma astrocyte samples. Taking into account the corresponding associations between the probe ID and gene symbols, the DEGs were identified prior to and subsequent to the summation of probe level values using the Limma package in R language, followed by Gene Ontology (GO) and pathway enrichment analyses. Interaction networks of the DEGs were constructed using the Biomolecular Interaction Network Database, and cluster analysis of the genes in the networks was performed using ClusterONE. Subsequent to the summation of probe value, a total of 223 genes were identified as DEGs between the normal and glaucoma samples, including 74 downregulated and 149 upregulated genes. In addition, the DEGs were found to be associated with several functions, including response to wounding, extracellular region part and calcium ion binding. The most significantly enriched pathways were complement and coagulation cascades, arrhythmogenic right ventricular cardiomyopathy and extracellular matrix (ECM)‑receptor interaction. Furthermore, interaction networks were constructed of the DEGs prior to and subsequent to the summation of probe values, and HNF4A and CEBPD were identified as hub genes. Additionally, 37 and 31 GO terms were identified to be enriched in the two DEGs of the networks prior to and subsequent to summation, respectively. The results indicated the identified genes associated with ECM as important, and the CEBPD gene was considered to be a critical gene in glaucoma. The findings of the present study offer a potential reference value in further investigations of glaucoma at the gene level.

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Related in: MedlinePlus

Gene expression analysis pre- and post-summation. (A) Scatter diagram of the gene expressing profiles (Aa) pre- and (Ab) post-summation. The log2FC value is on the x-axis and log10 (P-value) is on the y-axis. (B) Comparison between the number of genes pre- and post-summation. DEGs, differentially expressed genes; FC, fold-change; Up-DEGs, upregulated DEGs; Down-DEGs, downregulated DEGs.
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f1-mmr-12-04-4829: Gene expression analysis pre- and post-summation. (A) Scatter diagram of the gene expressing profiles (Aa) pre- and (Ab) post-summation. The log2FC value is on the x-axis and log10 (P-value) is on the y-axis. (B) Comparison between the number of genes pre- and post-summation. DEGs, differentially expressed genes; FC, fold-change; Up-DEGs, upregulated DEGs; Down-DEGs, downregulated DEGs.

Mentions: The MYH1, CSPG41 and GPR116 genes were identified to be the most significantly downregulated DEGs prior and subsequent to probe value summation. Similarly, among the upregulated genes, FGF7, ADH1B, CLU, ARR1C3, SEPP1 and PDE1A were in the top 10 significant DEGs. Scatter diagrams of pre- and post-summation data demonstrated that no significant difference existed in the number of DEGs (Fig. 1A). Excluding the repeated genes, the common DEGs pre- and post-summation of probe value were revealed using Venn analysis (Fig. 1B). A total of 128 common upregulated genes and 61 downregulated genes were identified. No genes contradicted each other in the four categories.


Bioinformatics analysis to identify the differentially expressed genes of glaucoma.

Yan X, Yuan F, Chen X, Dong C - Mol Med Rep (2015)

Gene expression analysis pre- and post-summation. (A) Scatter diagram of the gene expressing profiles (Aa) pre- and (Ab) post-summation. The log2FC value is on the x-axis and log10 (P-value) is on the y-axis. (B) Comparison between the number of genes pre- and post-summation. DEGs, differentially expressed genes; FC, fold-change; Up-DEGs, upregulated DEGs; Down-DEGs, downregulated DEGs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4581750&req=5

f1-mmr-12-04-4829: Gene expression analysis pre- and post-summation. (A) Scatter diagram of the gene expressing profiles (Aa) pre- and (Ab) post-summation. The log2FC value is on the x-axis and log10 (P-value) is on the y-axis. (B) Comparison between the number of genes pre- and post-summation. DEGs, differentially expressed genes; FC, fold-change; Up-DEGs, upregulated DEGs; Down-DEGs, downregulated DEGs.
Mentions: The MYH1, CSPG41 and GPR116 genes were identified to be the most significantly downregulated DEGs prior and subsequent to probe value summation. Similarly, among the upregulated genes, FGF7, ADH1B, CLU, ARR1C3, SEPP1 and PDE1A were in the top 10 significant DEGs. Scatter diagrams of pre- and post-summation data demonstrated that no significant difference existed in the number of DEGs (Fig. 1A). Excluding the repeated genes, the common DEGs pre- and post-summation of probe value were revealed using Venn analysis (Fig. 1B). A total of 128 common upregulated genes and 61 downregulated genes were identified. No genes contradicted each other in the four categories.

Bottom Line: In addition, the DEGs were found to be associated with several functions, including response to wounding, extracellular region part and calcium ion binding.The most significantly enriched pathways were complement and coagulation cascades, arrhythmogenic right ventricular cardiomyopathy and extracellular matrix (ECM)‑receptor interaction.Additionally, 37 and 31 GO terms were identified to be enriched in the two DEGs of the networks prior to and subsequent to summation, respectively.

View Article: PubMed Central - PubMed

Affiliation: Department of Ophthalmology, Pudong District Gongli Hospital, Shanghai 200135, P.R. China.

ABSTRACT
The aim of the present study was to screen the differentially expressed genes (DEGs) associated with glaucoma and investigate the changing patterns of the expression of these genes. The GSE2378 gene microarray data of glaucoma was downloaded from the Gene Expression Omnibus database, which included seven normal samples and eight glaucoma astrocyte samples. Taking into account the corresponding associations between the probe ID and gene symbols, the DEGs were identified prior to and subsequent to the summation of probe level values using the Limma package in R language, followed by Gene Ontology (GO) and pathway enrichment analyses. Interaction networks of the DEGs were constructed using the Biomolecular Interaction Network Database, and cluster analysis of the genes in the networks was performed using ClusterONE. Subsequent to the summation of probe value, a total of 223 genes were identified as DEGs between the normal and glaucoma samples, including 74 downregulated and 149 upregulated genes. In addition, the DEGs were found to be associated with several functions, including response to wounding, extracellular region part and calcium ion binding. The most significantly enriched pathways were complement and coagulation cascades, arrhythmogenic right ventricular cardiomyopathy and extracellular matrix (ECM)‑receptor interaction. Furthermore, interaction networks were constructed of the DEGs prior to and subsequent to the summation of probe values, and HNF4A and CEBPD were identified as hub genes. Additionally, 37 and 31 GO terms were identified to be enriched in the two DEGs of the networks prior to and subsequent to summation, respectively. The results indicated the identified genes associated with ECM as important, and the CEBPD gene was considered to be a critical gene in glaucoma. The findings of the present study offer a potential reference value in further investigations of glaucoma at the gene level.

Show MeSH
Related in: MedlinePlus