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Identification of hub genes and their SNP analysis in West Nile virus infection for designing therapeutic methodologies using RNA-Seq data

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Abstract

The West Nile virus (WNV) infections are generally asymptomatic and are considered as immediate concerns of biodefense due to the lack of any therapeutic remedies. In this work, we created an interaction network of 1159 differentially expressed genes to detect potential hub genes from WNV infected primary human macrophages. We go on to explore the genetic variations that can alter the expression and function of identified hub genes (HCLS1, SLC15A3, HCK, and LY96) using the PROVEAN Protein Batch tool and PolyPhen-2. Community analysis of the network revealed that these clusters were enriched in GO terms such as inflammatory response and regulation of proliferation. Analysis of hub genes can aid in determining their degree of conservation and may help us in understanding their functional roles in biological systems. The nsSNPs proposed in this work may be further targeted through experimental methods for improving treatment towards the infection of WNV.

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Acknowledgments

The Deanship of Scientific Research (DSR), King Abdulaziz University, Jeddah, funded this work under Grant No. (830-011-D1434). The authors, therefore, acknowledge with thanks DSR for technical and financial support.

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Authors declare no conflict of interest.

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Authors and Affiliations

  1. Faculty of Computing and Information Technology, King Abdulaziz University, Rabigh, 21911, Kingdom of Saudi Arabia

    Iftikhar Aslam Tayubi & Omar M. Barukab

  2. School of Chemistry and Biochemistry, Thapar University, Patiala, 147004, Punjab, India

    Ahmad Firoz

  3. Biomedical Informatics Center of ICMR, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India

    Ahmad Firoz

  4. Perdana University Centre for Bioinformatics, MARDI Complex, Jalan MAEPS Perdana, 43400, Serdang, Selangor, Malaysia

    Adeel Malik

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  1. Iftikhar Aslam Tayubi
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  4. Adeel Malik
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Correspondence to Iftikhar Aslam Tayubi.

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Tayubi, I.A., Firoz, A., Barukab, O.M. et al. Identification of hub genes and their SNP analysis in West Nile virus infection for designing therapeutic methodologies using RNA-Seq data. Genes Genom 37, 679–691 (2015). https://doi.org/10.1007/s13258-015-0297-y

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