1
|
Li L, Huang F, Zhang YH, Cai YD. Identifying allergic-rhinitis-associated genes with random-walk-based method in PPI network. Comput Biol Med 2024; 175:108495. [PMID: 38697003 DOI: 10.1016/j.compbiomed.2024.108495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/21/2024] [Accepted: 04/21/2024] [Indexed: 05/04/2024]
Abstract
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.
Collapse
Affiliation(s)
- Lin Li
- Department of Otolaryngology and Head&neck, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, China; Department of Otolaryngology and Head&neck, China-Japan Union Hospital, Jilin University, Changchun, 130033, China.
| | - FeiMing Huang
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
| |
Collapse
|
2
|
Li D, Li L, Quan F, Wang T, Xu S, Li S, Tian K, Feng M, He N, Tian L, Chen B, Zhang H, Wang L, Wang J. Identification of circulating immune landscape in ischemic stroke based on bioinformatics methods. Front Genet 2022; 13:921582. [PMID: 35957686 PMCID: PMC9358692 DOI: 10.3389/fgene.2022.921582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Ischemic stroke (IS) is a high-incidence disease that seriously threatens human life and health. Neuroinflammation and immune responses are key players in the pathophysiological processes of IS. However, the underlying immune mechanisms are not fully understood. In this study, we attempted to identify several immune biomarkers associated with IS. We first retrospectively collected validated human IS immune-related genes (IS-IRGs) as seed genes. Afterward, potential IS-IRGs were discovered by applying random walk with restart on the PPI network and the permutation test as a screening strategy. Doing so, the validated and potential sets of IS-IRGs were merged together as an IS-IRG catalog. Two microarray profiles were subsequently used to explore the expression patterns of the IS-IRG catalog, and only IS-IRGs that were differentially expressed between IS patients and controls in both profiles were retained for biomarker selection by the Random Forest rankings. CLEC4D and CD163 were finally identified as immune biomarkers of IS, and a classification model was constructed and verified based on the weights of two biomarkers obtained from the Neural Network algorithm. Furthermore, the CIBERSORT algorithm helped us determine the proportions of circulating immune cells. Correlation analyses between IS immune biomarkers and immune cell proportions demonstrated that CLEC4D was strongly correlated with the proportion of neutrophils (r = 0.72). These results may provide potential targets for further studies on immuno-neuroprotection therapies against reperfusion injury.
Collapse
Affiliation(s)
- Danyang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lifang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fei Quan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Tianfeng Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Si Xu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shuang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Kuo Tian
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Meng Feng
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ni He
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Liting Tian
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Biying Chen
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Huixue Zhang, ; Lihua Wang, ; Jianjian Wang,
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Huixue Zhang, ; Lihua Wang, ; Jianjian Wang,
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Huixue Zhang, ; Lihua Wang, ; Jianjian Wang,
| |
Collapse
|