Medical Journal of The Islamic Republic of Iran (MJIRI)
Iran University of Medical Sciences
Wed, Sep 11, 2024
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Volume 38, Issue 1 (1-2024)
Med J Islam Repub Iran 2024 |
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Hosseinpour Z, Rezaei Tavirani M, Akbari M E. Integrated Analysis of Multi-Omic Data Reveals Regulatory Mechanisms and Network Characteristics in Breast Cancer. Med J Islam Repub Iran 2024; 38 (1) :416-424
URL: http://mjiri.iums.ac.ir/article-1-8909-en.html
URL: http://mjiri.iums.ac.ir/article-1-8909-en.html
Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran , tavirani@sbmu.ac.ir
Abstract: (267 Views)
Background: Breast cancer is a complex and heterogeneous disease, and understanding its regulatory mechanisms and network characteristics is essential for identifying therapeutic targets and developing effective treatment strategies. This study aimed to unravel the intricate network of interactions involving differentially expressed genes, microribonucleic acid (miRNAs), and proteins in breast cancer through an integrative analysis of multi-omic data from Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) dataset.
Methods: The TCGA-BRCA dataset was used for data acquisition, which included RNA sequencing data for gene expression, miRNA sequencing data for miRNA expression, and protein expression quantification data. Various R packages, such as TCGAbiolinks, limma, and RPPA, were employed for data preprocessing and integration. Differential expression analysis, network construction, miRNA regulation exploration, pathway enrichment analysis, and independent dataset validation were performed.
Results: Eight consistently upregulated hub genes—including ACTB, HSP90AA1, FN1, HSPA8, CDC42, CDH1, UBC, and EP300—were identified in breast cancer, indicating their potential significance in driving the disease. Pathway enrichment analysis revealed highly enriched pathways in breast cancer, including proteoglycans in cancer, PI3K-Akt, and mitogen-activated protein kinase signaling.
Conclusion: This integrated multi-omic data analysis provides valuable insights into the regulatory mechanisms, network characteristics, and functional roles of genes, miRNAs, and proteins in breast cancer. The findings contribute to our understanding of the molecular landscape of breast cancer, facilitate the identification of potential therapeutic targets, and inform strategies for effective treatment.
Methods: The TCGA-BRCA dataset was used for data acquisition, which included RNA sequencing data for gene expression, miRNA sequencing data for miRNA expression, and protein expression quantification data. Various R packages, such as TCGAbiolinks, limma, and RPPA, were employed for data preprocessing and integration. Differential expression analysis, network construction, miRNA regulation exploration, pathway enrichment analysis, and independent dataset validation were performed.
Results: Eight consistently upregulated hub genes—including ACTB, HSP90AA1, FN1, HSPA8, CDC42, CDH1, UBC, and EP300—were identified in breast cancer, indicating their potential significance in driving the disease. Pathway enrichment analysis revealed highly enriched pathways in breast cancer, including proteoglycans in cancer, PI3K-Akt, and mitogen-activated protein kinase signaling.
Conclusion: This integrated multi-omic data analysis provides valuable insights into the regulatory mechanisms, network characteristics, and functional roles of genes, miRNAs, and proteins in breast cancer. The findings contribute to our understanding of the molecular landscape of breast cancer, facilitate the identification of potential therapeutic targets, and inform strategies for effective treatment.
Type of Study: Original Research |
Subject:
Computer scientist and technologist
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