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Network analysis reveals a stress-affected common gene module among seven stress-related diseases/systems which provides potential targets for mechanism research.

Guo L, Du Y, Wang J - Sci Rep (2015)

Bottom Line: This module is significantly overlapped with network that constructed by genes from the CS gene database. 36 genes with high connectivity (hub genes) were identified from seven networks as potential key genes in those diseases/systems, 33 of hub genes were included in the common module.Genes in the common module were enriched in 190 interactive gene ontology (GO) functional clusters which provide potential disease mechanism.In conclusion, by analyzing gene networks we revealed a stress-affected common gene module among seven stress-related diseases/systems which provides insight into the process of stress induction of disease and suggests potential gene and pathway candidates for further research.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China.

ABSTRACT
Chronic stress (CS) was reported to associate with many complex diseases and stress-related diseases show strong comorbidity; however, molecular analyses have not been performed to date to evaluate common stress-induced biological processes across these diseases. We utilized networks constructed by genes from seven genetic databases of stress-related diseases or systems to explore the common mechanisms. Genes were connected based on the interaction information of proteins they encode. A common sub-network constructed by 561 overlapping genes and 8863 overlapping edges among seven networks was identified and it provides a common gene module among seven stress-related diseases/systems. This module is significantly overlapped with network that constructed by genes from the CS gene database. 36 genes with high connectivity (hub genes) were identified from seven networks as potential key genes in those diseases/systems, 33 of hub genes were included in the common module. Genes in the common module were enriched in 190 interactive gene ontology (GO) functional clusters which provide potential disease mechanism. In conclusion, by analyzing gene networks we revealed a stress-affected common gene module among seven stress-related diseases/systems which provides insight into the process of stress induction of disease and suggests potential gene and pathway candidates for further research.

No MeSH data available.


a) Flowchart of gene network construction. Black nodes: seed nodes; striated nodes: first neighbors of seed nodes; and white nodes: other nodes in the STRING interactome. (b) The common sub-network among seven stress-related diseases/systems. (c) Largest functional GO group enriched by genes of stress-related disease/system common module.
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f1: a) Flowchart of gene network construction. Black nodes: seed nodes; striated nodes: first neighbors of seed nodes; and white nodes: other nodes in the STRING interactome. (b) The common sub-network among seven stress-related diseases/systems. (c) Largest functional GO group enriched by genes of stress-related disease/system common module.

Mentions: The database STRING 9.129 provides a comprehensive protein interactome that includes known and predicted protein-protein interactions scored according to their confidence. Information in this database was utilized to construct the disease/system and CS gene networks. Genes in the stress-related disease/system or CS datasets were considered seed nodes and used to obtain protein-protein interactions with the highest confidence (score >0.9). As shown in Fig. 1a, an extended network that included seed nodes, first neighbor nodes, and the highest confident interactions between these nodes was constructed for each gene set. All of the networks were visualized and analyzed with the visualization software Cytoscape 3.0.230. The node properties, such as the betweenness centrality (BC) and degree, were calculated using the plug-in “Network Analyzer”31 in the Cytoscape software. Hub genes were identified according to the following thresholds: BC > 0.05 and degree >5022. The statistical significant difference between properties of nodes in disease/system networks and the entire interactome was examined by T-test.


Network analysis reveals a stress-affected common gene module among seven stress-related diseases/systems which provides potential targets for mechanism research.

Guo L, Du Y, Wang J - Sci Rep (2015)

a) Flowchart of gene network construction. Black nodes: seed nodes; striated nodes: first neighbors of seed nodes; and white nodes: other nodes in the STRING interactome. (b) The common sub-network among seven stress-related diseases/systems. (c) Largest functional GO group enriched by genes of stress-related disease/system common module.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4526881&req=5

f1: a) Flowchart of gene network construction. Black nodes: seed nodes; striated nodes: first neighbors of seed nodes; and white nodes: other nodes in the STRING interactome. (b) The common sub-network among seven stress-related diseases/systems. (c) Largest functional GO group enriched by genes of stress-related disease/system common module.
Mentions: The database STRING 9.129 provides a comprehensive protein interactome that includes known and predicted protein-protein interactions scored according to their confidence. Information in this database was utilized to construct the disease/system and CS gene networks. Genes in the stress-related disease/system or CS datasets were considered seed nodes and used to obtain protein-protein interactions with the highest confidence (score >0.9). As shown in Fig. 1a, an extended network that included seed nodes, first neighbor nodes, and the highest confident interactions between these nodes was constructed for each gene set. All of the networks were visualized and analyzed with the visualization software Cytoscape 3.0.230. The node properties, such as the betweenness centrality (BC) and degree, were calculated using the plug-in “Network Analyzer”31 in the Cytoscape software. Hub genes were identified according to the following thresholds: BC > 0.05 and degree >5022. The statistical significant difference between properties of nodes in disease/system networks and the entire interactome was examined by T-test.

Bottom Line: This module is significantly overlapped with network that constructed by genes from the CS gene database. 36 genes with high connectivity (hub genes) were identified from seven networks as potential key genes in those diseases/systems, 33 of hub genes were included in the common module.Genes in the common module were enriched in 190 interactive gene ontology (GO) functional clusters which provide potential disease mechanism.In conclusion, by analyzing gene networks we revealed a stress-affected common gene module among seven stress-related diseases/systems which provides insight into the process of stress induction of disease and suggests potential gene and pathway candidates for further research.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China.

ABSTRACT
Chronic stress (CS) was reported to associate with many complex diseases and stress-related diseases show strong comorbidity; however, molecular analyses have not been performed to date to evaluate common stress-induced biological processes across these diseases. We utilized networks constructed by genes from seven genetic databases of stress-related diseases or systems to explore the common mechanisms. Genes were connected based on the interaction information of proteins they encode. A common sub-network constructed by 561 overlapping genes and 8863 overlapping edges among seven networks was identified and it provides a common gene module among seven stress-related diseases/systems. This module is significantly overlapped with network that constructed by genes from the CS gene database. 36 genes with high connectivity (hub genes) were identified from seven networks as potential key genes in those diseases/systems, 33 of hub genes were included in the common module. Genes in the common module were enriched in 190 interactive gene ontology (GO) functional clusters which provide potential disease mechanism. In conclusion, by analyzing gene networks we revealed a stress-affected common gene module among seven stress-related diseases/systems which provides insight into the process of stress induction of disease and suggests potential gene and pathway candidates for further research.

No MeSH data available.