Gene Co-expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Vitiligo Disease: A Systems Biology Study
Vitiligo is the most common cause of skin, hair, and oral depigmentation which is known as an autoimmune disorder. Genetic and environmental factors have important roles in the progression of the disease. Dysregulation of gene expression, like microRNAs (miRNA), may serve as major relevant factors....
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Tehran University of Medical Sciences
2020-10-01
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| Series: | Iranian Journal of Allergy, Asthma and Immunology |
| Subjects: | |
| Online Access: | https://ijaai.tums.ac.ir/index.php/ijaai/article/view/2686 |
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| author | Afshin Derakhshani Homa Mollaei Negin Parsamanesh Mohammad Fereidouni Ebrahim Miri-Moghaddam Saeed Nasseri Yongwen Luo Hossein Safarpour Behzad Baradaran |
| author_facet | Afshin Derakhshani Homa Mollaei Negin Parsamanesh Mohammad Fereidouni Ebrahim Miri-Moghaddam Saeed Nasseri Yongwen Luo Hossein Safarpour Behzad Baradaran |
| author_sort | Afshin Derakhshani |
| collection | DOAJ |
| description | Vitiligo is the most common cause of skin, hair, and oral depigmentation which is known as an autoimmune disorder. Genetic and environmental factors have important roles in the progression of the disease. Dysregulation of gene expression, like microRNAs (miRNA), may serve as major relevant factors. Several biological processes are involved in vitiligo disease and developing a comprehensive approach helps us to better understand the molecular mechanisms of disease.
In this research, we describe how a weighted gene co-expression network analysis as a systems biology approach assists to define the primary gene modules, hub genes, and messenger RNA (mRNA)-miRNA regulatory network in vitiligo disease as the novel biomarkers.
The results demonstrated a module with a high correlation with vitiligo state. Moreover, gene enrichment analysis showed that this module's genes were mostly involved in some biological activities including G protein-coupled receptors signaling pathway, lymphocyte chemotaxis, chemokine activity, neutrophil migration, granulocyte chemotaxis, etc. The co-expression network was constructed using top hub genes of the correlated module which are named as CXCL10, ARL9, AKR1B10, COX7B, RPL26, SPA17, NDUFAF2, RPF2, DAPL1, RPL34, CWC15, NDUFB3, RPL26L1, ACOT13, HSPB11, and NSA2. MicroRNAs prediction tool (miRWalk) revealed top miRNAs correlated with the interested module. Finally, a drug-target network was constructed which indicated interactions of some food and drug administration (FDA) approved drugs with hub genes.
Our findings specified one important module and main hub genes which can be considered as novel biomarkers for vitiligo therapeutic purposes. |
| first_indexed | 2024-12-12T21:21:59Z |
| format | Article |
| id | doaj.art-46a4bf35b928442a8e5df2af08826a91 |
| institution | Directory Open Access Journal |
| issn | 1735-1502 1735-5249 |
| language | English |
| last_indexed | 2024-12-12T21:21:59Z |
| publishDate | 2020-10-01 |
| publisher | Tehran University of Medical Sciences |
| record_format | Article |
| series | Iranian Journal of Allergy, Asthma and Immunology |
| spelling | doaj.art-46a4bf35b928442a8e5df2af08826a912022-12-22T00:11:33ZengTehran University of Medical SciencesIranian Journal of Allergy, Asthma and Immunology1735-15021735-52492020-10-0119510.18502/ijaai.v19i5.44672686Gene Co-expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Vitiligo Disease: A Systems Biology StudyAfshin Derakhshani0Homa Mollaei1Negin Parsamanesh2Mohammad Fereidouni3Ebrahim Miri-Moghaddam4Saeed Nasseri5Yongwen Luo6Hossein Safarpour7Behzad Baradaran8Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, IranDepartment of Biology, Faculty of Sciences, University of Birjand, Birjand, IranZanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, IranCellular and Molecular Research center, Birjand University of Medical Sciences, Birjand, IranDepartment of Molecular Medicine, Cardiovascular Diseases Research Center, School of Medicine, Birjand University of Medical Sciences, Birjand, IranCellular and Molecular Research center, Birjand University of Medical Sciences, Birjand, IranDepartment of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, ChinaCellular and Molecular Research center, Birjand University of Medical Sciences, Birjand, IranImmunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran AND Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, IranVitiligo is the most common cause of skin, hair, and oral depigmentation which is known as an autoimmune disorder. Genetic and environmental factors have important roles in the progression of the disease. Dysregulation of gene expression, like microRNAs (miRNA), may serve as major relevant factors. Several biological processes are involved in vitiligo disease and developing a comprehensive approach helps us to better understand the molecular mechanisms of disease. In this research, we describe how a weighted gene co-expression network analysis as a systems biology approach assists to define the primary gene modules, hub genes, and messenger RNA (mRNA)-miRNA regulatory network in vitiligo disease as the novel biomarkers. The results demonstrated a module with a high correlation with vitiligo state. Moreover, gene enrichment analysis showed that this module's genes were mostly involved in some biological activities including G protein-coupled receptors signaling pathway, lymphocyte chemotaxis, chemokine activity, neutrophil migration, granulocyte chemotaxis, etc. The co-expression network was constructed using top hub genes of the correlated module which are named as CXCL10, ARL9, AKR1B10, COX7B, RPL26, SPA17, NDUFAF2, RPF2, DAPL1, RPL34, CWC15, NDUFB3, RPL26L1, ACOT13, HSPB11, and NSA2. MicroRNAs prediction tool (miRWalk) revealed top miRNAs correlated with the interested module. Finally, a drug-target network was constructed which indicated interactions of some food and drug administration (FDA) approved drugs with hub genes. Our findings specified one important module and main hub genes which can be considered as novel biomarkers for vitiligo therapeutic purposes.https://ijaai.tums.ac.ir/index.php/ijaai/article/view/2686MicroRNAsSystems biologyVitiligo |
| spellingShingle | Afshin Derakhshani Homa Mollaei Negin Parsamanesh Mohammad Fereidouni Ebrahim Miri-Moghaddam Saeed Nasseri Yongwen Luo Hossein Safarpour Behzad Baradaran Gene Co-expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Vitiligo Disease: A Systems Biology Study Iranian Journal of Allergy, Asthma and Immunology MicroRNAs Systems biology Vitiligo |
| title | Gene Co-expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Vitiligo Disease: A Systems Biology Study |
| title_full | Gene Co-expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Vitiligo Disease: A Systems Biology Study |
| title_fullStr | Gene Co-expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Vitiligo Disease: A Systems Biology Study |
| title_full_unstemmed | Gene Co-expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Vitiligo Disease: A Systems Biology Study |
| title_short | Gene Co-expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Vitiligo Disease: A Systems Biology Study |
| title_sort | gene co expression network analysis for identifying modules and functionally enriched pathways in vitiligo disease a systems biology study |
| topic | MicroRNAs Systems biology Vitiligo |
| url | https://ijaai.tums.ac.ir/index.php/ijaai/article/view/2686 |
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