Research Article

Topological centrality-based identification of hub genes and pathways associated with acute viral respiratory infection in infants

Published: December 28, 2015
Genet. Mol. Res. 14 (4) : 18334-18343 DOI: 10.4238/2015.December.23.21

Abstract

The objective of this study was to identify hub genes and pathways associated with acute respiratory infection (ARI) in infants based on gene expression profiles. Differentially expressed genes (DEGs) between ARI and normal (controls) infants were identified based on linear modeling of the microarray data using Limma package. A protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/proteins and clusters were obtained by employing the molecular complex detection algorithm. Topological centrality was applied to characterize the biological importance of genes in the network. Functional enrichment analysis of the genes was performed based on the expression analysis systematic explore test. In total, 116 DEGs between ARI and controls were identified. Of the 61 nodes and 189 edges in the PPI network generated with the DEGs, three clusters were mined. Six hub genes namely RPL6, RPL3, EEF1B2, RPL15, EEF1A1, and RPS2, which were identified based on the topological centrality measures, were evaluated further. Functional enrichment analysis revealed that DEGs were significantly enriched in terms of Gene Ontology translational elongation, structural constituent of ribosome, and cytosol. The most significant term of pathway analysis was “ribosome”. In summary, this study suggests RPL6, RPL3, and RPL15 as hub genes and the ribosome pathway to be significantly associated with viral ARI in infants, which might also be used as potential markers for the viral etiology.

The objective of this study was to identify hub genes and pathways associated with acute respiratory infection (ARI) in infants based on gene expression profiles. Differentially expressed genes (DEGs) between ARI and normal (controls) infants were identified based on linear modeling of the microarray data using Limma package. A protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/proteins and clusters were obtained by employing the molecular complex detection algorithm. Topological centrality was applied to characterize the biological importance of genes in the network. Functional enrichment analysis of the genes was performed based on the expression analysis systematic explore test. In total, 116 DEGs between ARI and controls were identified. Of the 61 nodes and 189 edges in the PPI network generated with the DEGs, three clusters were mined. Six hub genes namely RPL6, RPL3, EEF1B2, RPL15, EEF1A1, and RPS2, which were identified based on the topological centrality measures, were evaluated further. Functional enrichment analysis revealed that DEGs were significantly enriched in terms of Gene Ontology translational elongation, structural constituent of ribosome, and cytosol. The most significant term of pathway analysis was “ribosome”. In summary, this study suggests RPL6, RPL3, and RPL15 as hub genes and the ribosome pathway to be significantly associated with viral ARI in infants, which might also be used as potential markers for the viral etiology.

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