Network visualization and identifying hub genes involved in the foot-and-mouth disease in Holstein dairy cows

Articles in Press

Document Type : Research Article (Regular Paper)

Author

Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran

Abstract

Abstract
Foot-and-mouth disease (FMD) is a dangerous disease in ruminants that causes severe production reduction in adult livestock and mortality in lambs and calves. In this study, the GSE83514 dataset (samples of nasopharyngeal epithelium from Holstein cattle) was extracted from the GEO database and was analyzed to identify gene network, hub genes and gene clusters underlying foot-and-mouth disease in dairy cows. Before performing any analysis, data quality control and normalization were performed using the online software GEO2R and genes with differential expression between the two treatments of healthy and patient samples at a probability level of P-value < 0.05 and Log Foldchange statistic [-2< LogFC< +2] were identified. We employed CytoNCA and cytoHuba plugins within Cytoscape software for network analysis. The MCL algorithm was used to identify five main clusters in the body of gene network. The results revealed 249 genes with significant expression differences (120 upregulated genes and 129 down-regulated genes). Five main clusters linked to signaling pathways associated with chemokines, tumor necrosis factor-alpha (TNF-α), and suppressor of viral growth were detected in the body of gene network. Ten genes CD9, ICOS, CXCL9, CD2, TTN, PTPRC, CALML5, IRF8, CD40, CXCR5 were identified as the hub genes which closely linked to key pathways involved in FMD infection. These genes were active mainly in hematopoietic system, lymphoid tissue and blood and involved in importance biological process such as immune system process, lymphocyte activation, positive regulation of cytokine production and B cell activation. These genes can be used as genetic markers, making them valuable for increasing genetic resistance to FMD.

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References

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Journal of Livestock Science and Technologies

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Available Online from 11 July 2026

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