Article
Open Access
Volume 4 · Issue 4 · 2024
pp. 208–217
Gene Expression Profiling in Breast Cancer: Responses to Radiation Therapy
Meenakshi Upadhyay1 
, Surbhi Singh2 , Seema Khanna1 , Suchitra Singh2 , Royana Singh2
, Surbhi Singh2 , Seema Khanna1 , Suchitra Singh2 , Royana Singh2
1
Department of General Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
2
Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
Abstract
Objectives: This study aims to investigate the gene expression in breast cancer (BC) in response to radiation therapy using GEO2R analysis of datasets from the Gene Expression Omnibus database.
Methods: The data used in the research was obtained from the GEO of the GSE 59732 and GSE 59734 gene expression datasets. These datasets included various breast cancer treated with radiation therapy. DEGs (Differentially expressed genes) were identified using GEO2R of p-value less than 0.05 and a log FC threshold of 1.2. STRING was used to generate PPI (protein-protein interaction) networks, while Cytoscape software was used to identify important hub genes. The Enrichr tool was used to analyze Gene Ontology and KEGG pathway and network analyst tool was used to study gene-disease association.
Results: A total of 61 upregulated DEGs common in both datasets were observed in the study. Gene ontology analysis revealed that biological processes mostly enriched in regulation of peptidyl-tyrosin phosphorylation, cellular components mainly enriched in phosphatase binding. Proteoglycans in cancer found in both KEGG pathway and gene-disease association pathways.
Conclusion: The study identified DEGs in breast cancer in response to radiation therapy. Key hub genes, particularly EGFR and MAPK3, were linked to many cancer-related pathways including breast cancer.
Methods: The data used in the research was obtained from the GEO of the GSE 59732 and GSE 59734 gene expression datasets. These datasets included various breast cancer treated with radiation therapy. DEGs (Differentially expressed genes) were identified using GEO2R of p-value less than 0.05 and a log FC threshold of 1.2. STRING was used to generate PPI (protein-protein interaction) networks, while Cytoscape software was used to identify important hub genes. The Enrichr tool was used to analyze Gene Ontology and KEGG pathway and network analyst tool was used to study gene-disease association.
Results: A total of 61 upregulated DEGs common in both datasets were observed in the study. Gene ontology analysis revealed that biological processes mostly enriched in regulation of peptidyl-tyrosin phosphorylation, cellular components mainly enriched in phosphatase binding. Proteoglycans in cancer found in both KEGG pathway and gene-disease association pathways.
Conclusion: The study identified DEGs in breast cancer in response to radiation therapy. Key hub genes, particularly EGFR and MAPK3, were linked to many cancer-related pathways including breast cancer.
Keywords: Breast Cancer, DEGs, gene ontology, hub genes, radiation therapy, gene expression omnibus
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