(2020) Assessment of the genes and molecular mechanisms of B cells activation through systems biology approaches. Human Antibodies. pp. 83-87. ISSN 10932607 (ISSN)
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Abstract
Two classes of T helper lymphocytes, Th1 and Th2, have different roles in B cell activation based on specific cytokines. To understand the difference of molecular mechanisms of B cell activation, the microarray dataset of B cells co-cultured with type 1 and 2 T helper, Be1 and Be2, were investigated. After quality assessment, using the GEO2R tool, the GSE84948 dataset was re-analyzed. Genes with adjusted p-value ⩽0.05 were assumed as differentially expressed (DE). The protein-protein interaction (PPI) networks were constructed using CluePedia plugin of Cytoscape, and analyzed by NetworkAnalyzer tool and MCODE plugin. Using ClueGO plugin of Cytoscape software, gene ontology (GO) analysis was performed. The comparison of Be1 and Be2 cells with naive B cells revealed 8742 and 8748 DE genes, respectively. The topology analysis of PPI networks predicted central genes. Among these, Jak3, Actrt3, and Pik3cb genes were determined as crucial genes in Be1 network. Prkx, Smarca4, and Jak2 genes were defined as critical genes in Be2 PPI network. GO analysis with PPI networks genes resulted in the promotion of immune system activation. In conclusion, we explored holistic methods for molecular assay of the difference between B cell activation mechanisms with Th1 and Th2. ©½ 0.05 were assumed as differentially expressed (DE). The protein-protein interaction (PPI) networks were constructed using CluePedia plugin of Cytoscape, and analyzed by NetworkAnalyzer tool and MCODE plugin. Using ClueGO plugin of Cytoscape software, gene ontology (GO) analysis was performed. The comparison of Be1 and Be2 cells with naive B cells revealed 8742 and 8748 DE genes, respectively. The topology analysis of PPI networks predicted central genes. Among these, Jak3, Actrt3, and Pik3cb genes were determined as crucial genes in Be1 network. Prkx, Smarca4, and Jak2 genes were defined as critical genes in Be2 PPI network. GO analysis with PPI networks genes resulted in the promotion of immune system activation. In conclusion, we explored holistic methods for molecular assay of the difference between B cell activation mechanisms with Th1 and Th2. © 2020-IOS Press and the authors. All rights reserved.
| Item Type: | Article |
|---|---|
| Keywords: | cytokines gene ontology helper-Inducer microarray protein interaction network T-Lymphocytes immunoglobulin enhancer binding protein actrt3 gene Article B lymphocyte activation bioinformatics cell activation cell differentiation cell migration gene gene expression genetic analysis human immune response immune system jak 3 gene Jak2 gene microarray analysis morphogenesis Pik3cb gene priority journal Prkx gene protein localization protein polymerization protein protein interaction quality control regulatory mechanism signal transduction Smarca4 gene systems biology T lymphocyte activation Th2 cell B lymphocyte genetics immunology lymphocyte activation protein analysis Th1 cell B-Lymphocytes Humans Protein Interaction Maps Th1 Cells Th2 Cells |
| Subjects: | QU Biochemistry. Cell Biology and Genetics > QU 300-560 Cell Biology and Genetics |
| Divisions: | Faculty of Medicine > Department of Basic Science > Department of Molecular Medicine and Genetics |
| Page Range: | pp. 83-87 |
| Journal or Publication Title: | Human Antibodies |
| Journal Index: | Scopus |
| Volume: | 28 |
| Number: | 1 |
| Identification Number: | https://doi.org/10.3233/HAB-190393 |
| ISSN: | 10932607 (ISSN) |
| Depositing User: | Zahra Otroj |
| URI: | http://eprints.mui.ac.ir/id/eprint/12523 |
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