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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

Interaction networks of the DEGs. (A) Pre-summation network; (Aa) whole network; (Ab) most significant subnetwork. (B) post-summation network; (Ba) whole network; (Bb) most significant subnetwork. Pink nodes represent DEGs; blue nodes represent their interaction genes. Red arrows indicate the interaction between protein and DNA, blue lines indicate interaction between proteins. DEGs, differentially expressed genes.
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f2-mmr-12-04-4829: Interaction networks of the DEGs. (A) Pre-summation network; (Aa) whole network; (Ab) most significant subnetwork. (B) post-summation network; (Ba) whole network; (Bb) most significant subnetwork. Pink nodes represent DEGs; blue nodes represent their interaction genes. Red arrows indicate the interaction between protein and DNA, blue lines indicate interaction between proteins. DEGs, differentially expressed genes.

Mentions: The DEGs were mapped to the BIND database and significant interactions were screened with a confidence coefficient >0.7. By integrating these associations, interaction networks of the DEGs were constructed. In the networks of DEGs prior to summation (Fig. 2Aa), HNF4A was connected with multiple modules. The protein in the network serves as a node, and the degree of a node denotes the number of proteins interacting with the specific node, which is indicated by the lines between them. The 'hub nodes' were defined as the nodes which had high degrees within the network. The IGF1R, RUNX1T1 and STAT1 DEGs were identified as hub nodes. Following cluster analysis using ClusterONE, a module containing FOS and CEBPD DEGs, and non-DEGs belonging to the HNF4A and CEBP families, were obtained (Fig. 2Ab). The module contained a total of 18 nodes, with a module density of 0.542, quality of 0.874 and P-value of 2.222E-7.


Bioinformatics analysis to identify the differentially expressed genes of glaucoma.

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

Interaction networks of the DEGs. (A) Pre-summation network; (Aa) whole network; (Ab) most significant subnetwork. (B) post-summation network; (Ba) whole network; (Bb) most significant subnetwork. Pink nodes represent DEGs; blue nodes represent their interaction genes. Red arrows indicate the interaction between protein and DNA, blue lines indicate interaction between proteins. DEGs, differentially expressed genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2-mmr-12-04-4829: Interaction networks of the DEGs. (A) Pre-summation network; (Aa) whole network; (Ab) most significant subnetwork. (B) post-summation network; (Ba) whole network; (Bb) most significant subnetwork. Pink nodes represent DEGs; blue nodes represent their interaction genes. Red arrows indicate the interaction between protein and DNA, blue lines indicate interaction between proteins. DEGs, differentially expressed genes.
Mentions: The DEGs were mapped to the BIND database and significant interactions were screened with a confidence coefficient >0.7. By integrating these associations, interaction networks of the DEGs were constructed. In the networks of DEGs prior to summation (Fig. 2Aa), HNF4A was connected with multiple modules. The protein in the network serves as a node, and the degree of a node denotes the number of proteins interacting with the specific node, which is indicated by the lines between them. The 'hub nodes' were defined as the nodes which had high degrees within the network. The IGF1R, RUNX1T1 and STAT1 DEGs were identified as hub nodes. Following cluster analysis using ClusterONE, a module containing FOS and CEBPD DEGs, and non-DEGs belonging to the HNF4A and CEBP families, were obtained (Fig. 2Ab). The module contained a total of 18 nodes, with a module density of 0.542, quality of 0.874 and P-value of 2.222E-7.

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