MiRNA target enrichment analysis of co-expression network modules reveals important miRNAs and their roles in breast cancer progression
Breast cancer has the highest incidence and is the fifth cause of death in cancers. Progression is one of the important features of breast cancer which makes it a life-threatening cancer. MicroRNAs are small RNA molecules that have pivotal roles in the regulation of gene expression and they control...
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| Format: | Article |
| Language: | English |
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De Gruyter
2024-12-01
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| Series: | Journal of Integrative Bioinformatics |
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| Online Access: | https://doi.org/10.1515/jib-2022-0036 |
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| _version_ | 1841556518442369024 |
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| author | Bazyari Mohammad Javad Aghaee-Bakhtiari Seyed Hamid |
| author_facet | Bazyari Mohammad Javad Aghaee-Bakhtiari Seyed Hamid |
| author_sort | Bazyari Mohammad Javad |
| collection | DOAJ |
| description | Breast cancer has the highest incidence and is the fifth cause of death in cancers. Progression is one of the important features of breast cancer which makes it a life-threatening cancer. MicroRNAs are small RNA molecules that have pivotal roles in the regulation of gene expression and they control different properties in breast cancer such as progression. Recently, systems biology offers novel approaches to study complicated biological systems like miRNAs to find their regulatory roles. One of these approaches is analysis of weighted co-expression network in which genes with similar expression patterns are considered as a single module. Because the genes in one module have similar expression, it is rational to think the same regulatory elements such as miRNAs control their expression. Herein, we use WGCNA to find important modules related to breast cancer progression and use hypergeometric test to perform miRNA target enrichment analysis and find important miRNAs. Also, we use negative correlation between miRNA expression and modules as the second filter to ensure choosing the right candidate miRNAs regarding to important modules. We found hsa-mir-23b, hsa-let-7b and hsa-mir-30a are important miRNAs in breast cancer and also investigated their roles in breast cancer progression. |
| format | Article |
| id | doaj-art-a4e80e8341bc48e3a919f273e6a0e28d |
| institution | Kabale University |
| issn | 1613-4516 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj-art-a4e80e8341bc48e3a919f273e6a0e28d2025-01-07T07:55:54ZengDe GruyterJournal of Integrative Bioinformatics1613-45162024-12-012142094910.1515/jib-2022-0036MiRNA target enrichment analysis of co-expression network modules reveals important miRNAs and their roles in breast cancer progressionBazyari Mohammad Javad0Aghaee-Bakhtiari Seyed Hamid1Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, 37552Mashhad University of Medical Sciences, Mashhad, IranBioinformatics Research Center,Basic Sciences Research Institute, 37552Mashhad University of Medical Sciences, Mashhad, IranBreast cancer has the highest incidence and is the fifth cause of death in cancers. Progression is one of the important features of breast cancer which makes it a life-threatening cancer. MicroRNAs are small RNA molecules that have pivotal roles in the regulation of gene expression and they control different properties in breast cancer such as progression. Recently, systems biology offers novel approaches to study complicated biological systems like miRNAs to find their regulatory roles. One of these approaches is analysis of weighted co-expression network in which genes with similar expression patterns are considered as a single module. Because the genes in one module have similar expression, it is rational to think the same regulatory elements such as miRNAs control their expression. Herein, we use WGCNA to find important modules related to breast cancer progression and use hypergeometric test to perform miRNA target enrichment analysis and find important miRNAs. Also, we use negative correlation between miRNA expression and modules as the second filter to ensure choosing the right candidate miRNAs regarding to important modules. We found hsa-mir-23b, hsa-let-7b and hsa-mir-30a are important miRNAs in breast cancer and also investigated their roles in breast cancer progression.https://doi.org/10.1515/jib-2022-0036systems biologygene expression regulationfunctional enrichment analysisprotein-protein interaction networkmolecular complex detection |
| spellingShingle | Bazyari Mohammad Javad Aghaee-Bakhtiari Seyed Hamid MiRNA target enrichment analysis of co-expression network modules reveals important miRNAs and their roles in breast cancer progression Journal of Integrative Bioinformatics systems biology gene expression regulation functional enrichment analysis protein-protein interaction network molecular complex detection |
| title | MiRNA target enrichment analysis of co-expression network modules reveals important miRNAs and their roles in breast cancer progression |
| title_full | MiRNA target enrichment analysis of co-expression network modules reveals important miRNAs and their roles in breast cancer progression |
| title_fullStr | MiRNA target enrichment analysis of co-expression network modules reveals important miRNAs and their roles in breast cancer progression |
| title_full_unstemmed | MiRNA target enrichment analysis of co-expression network modules reveals important miRNAs and their roles in breast cancer progression |
| title_short | MiRNA target enrichment analysis of co-expression network modules reveals important miRNAs and their roles in breast cancer progression |
| title_sort | mirna target enrichment analysis of co expression network modules reveals important mirnas and their roles in breast cancer progression |
| topic | systems biology gene expression regulation functional enrichment analysis protein-protein interaction network molecular complex detection |
| url | https://doi.org/10.1515/jib-2022-0036 |
| work_keys_str_mv | AT bazyarimohammadjavad mirnatargetenrichmentanalysisofcoexpressionnetworkmodulesrevealsimportantmirnasandtheirrolesinbreastcancerprogression AT aghaeebakhtiariseyedhamid mirnatargetenrichmentanalysisofcoexpressionnetworkmodulesrevealsimportantmirnasandtheirrolesinbreastcancerprogression |