Identifying allergic-rhinitis-associated genes with random-walk-based method in PPI network

被引：1
作者：
Li L. [1 ,2 ]
Huang F. [3 ]
Zhang Y.-H. [4 ]
Cai Y.-D. [3 ]
机构：
[1] Department of Otolaryngology and Head&neck, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi Medical Center, Nanjing Medical University, Wuxi
[2] Department of Otolaryngology and Head&neck, China-Japan Union Hospital, Jilin University, Changchun
[3] School of Life Sciences, Shanghai University, Shanghai
[4] Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, 02115, MA
来源：
Computers in Biology and Medicine | 2024年 / 175卷
关键词：
Allergic rhinitis; Disease gene; Protein-protein interaction; Random walk with restart;
D O I：
10.1016/j.compbiomed.2024.108495
中图分类号：
学科分类号：
摘要：
Allergic rhinitis is a common allergic disease with a complex pathogenesis and many unresolved issues. Studies have shown that the incidence of allergic rhinitis is closely related to genetic factors, and research on the related genes could help further understand its pathogenesis and develop new treatment methods. In this study, 446 allergic rhinitis-related genes were obtained on the basis of the DisGeNET database. The protein–protein interaction network was searched using the random-walk-with-restart algorithm with these 446 genes as seed nodes to assess the linkages between other genes and allergic rhinitis. Then, this result was further examined by three screening tests, including permutation, interaction, and enrichment tests, which aimed to pick up genes that have strong and special associations with allergic rhinitis. 52 novel genes were finally obtained. The functional enrichment test confirmed their relationships to the biological processes and pathways related to allergic rhinitis. Furthermore, some genes were extensively analyzed to uncover their special or latent associations to allergic rhinitis, including IRAK2 and MAPK, which are involved in the pathogenesis of allergic rhinitis and the inhibition of allergic inflammation via the p38-MAPK pathway, respectively. The new found genes may help the following investigations for understanding the underlying molecular mechanisms of allergic rhinitis and developing effective treatments. © 2024 Elsevier Ltd
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共 70 条
[1]  
Bernstein D.I., Schwartz G., Bernstein J.A., Allergic rhinitis: mechanisms and treatment, Immunol. Allergy Clin., 36, pp. 261-278, (2016)
[2]  
Drazdauskaite G., Layhadi J.A., Shamji M.H., Mechanisms of allergen immunotherapy in allergic rhinitis, Curr. Allergy Asthma Rep., 21, (2020)
[3]  
Greiner A.N., Hellings P.W., Rotiroti G., Scadding G.K., Allergic rhinitis, Lancet, 378, pp. 2112-2122, (2011)
[4]  
Skoner D.P., Allergic rhinitis: definition, epidemiology, pathophysiology, detection, and diagnosis, J. Allergy Clin. Immunol., 108, pp. S2-S8, (2001)
[5]  
Wheatley L.M., Togias A., Allergic rhinitis, N. Engl. J. Med., 372, pp. 456-463, (2015)
[6]  
Wang D.-Y., Risk factors of allergic rhinitis: genetic or environmental?, Therapeut. Clin. Risk Manag., 1, (2005)
[7]  
Chen R.-X., Dai M.-D., Zhang Q.-Z., Lu M.-P., Wang M.-L., Yin M., Zhu X.-J., Wu Z.-F., Zhang Z.-D., Cheng L., TLR signaling pathway gene polymorphisms, gene–gene and gene–environment interactions in allergic rhinitis, J. Inflamm. Res., pp. 3613-3630, (2022)
[8]  
Yuan J., Liu Y., Yu J., Dai M., Zhu Y., Bao Y., Peng H., Liu K., Zhu X., Gene knockdown of CCR3 reduces eosinophilic inflammation and the Th2 immune response by inhibiting the PI3K/AKT pathway in allergic rhinitis mice, Sci. Rep., 12, (2022)
[9]  
Falahi S., Mortazavi S.H.R., Salari F., Koohyanizadeh F., Rezaeimanesh A., Gorgin Karaji A., Association between IL-33 gene polymorphism (Rs7044343) and risk of allergic rhinitis, Immunol. Invest., 51, pp. 29-39, (2022)
[10]  
Ruan W., Liu R., Yang H., Ren J., Liu Y., Genetic loci in phospholipase C-like 1 (PLCL1) are protective factors for allergic rhinitis in han population of northern shaanxi, China, J. Asthma Allergy, 15, pp. 1321-1335, (2022)
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