en Computer scientist and technologist Computer scientist and technologist Original Research Original Research <span style="font-size:13pt"><span style="text-justify:kashida"><span style="text-kashida:0%"><span style="text-autospace:none"><span new="" roman="" style="font-family:" times=""><span style="font-style:italic"><b><span style="font-size:9.0pt"><span style="font-style:normal">Background: </span></span></b><span style="font-size:9.0pt"><span style="font-style:normal">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.</span></span></span></span></span></span></span></span><br> <span style="font-size:13pt"><span style="text-justify:kashida"><span style="text-kashida:0%"><span style="text-autospace:none"><span new="" roman="" style="font-family:" times=""><span style="font-style:italic"><span style="font-size:9.0pt"><span style="font-style:normal">&nbsp;&nbsp; <b>Methods:</b> 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.</span></span></span></span></span></span></span></span><br> <span style="font-size:13pt"><span style="text-justify:kashida"><span style="text-kashida:0%"><span style="text-autospace:none"><span new="" roman="" style="font-family:" times=""><span style="font-style:italic"><span style="font-size:9.0pt"><span style="font-style:normal">&nbsp;&nbsp; <b>Results:</b> Eight consistently upregulated hub genes&mdash;including ACTB, HSP90AA1, FN1, HSPA8, CDC42, CDH1, UBC, and EP300&mdash;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. </span></span></span></span></span></span></span></span><br> <span style="font-size:13pt"><span style="text-justify:kashida"><span style="text-kashida:0%"><span style="text-autospace:none"><span new="" roman="" style="font-family:" times=""><span style="font-style:italic"><span style="font-size:9.0pt"><span style="font-style:normal">&nbsp;&nbsp; <b>Conclusion: </b>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.</span></span></span></span></span></span></span></span><br> &nbsp; Breast Cancer, Target Therapy, Multiomic, Hub-Genes 416 424 http://mjiri.iums.ac.ir/browse.php?a_code=A-10-8432-1&slc_lang=en&sid=1 Zahra Hosseinpour hosseinpour_z@yahoo.com 200319475328460089324 200319475328460089324 No Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran Mostafa Rezaei Tavirani tavirani@sbmu.ac.ir 200319475328460089325 200319475328460089325 Yes Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran Mohammad Esmaeil Akbari profmeakbari@gmail.com 200319475328460089326 200319475328460089326 No Surgical Oncology, Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran