Exploring Breast Cancer-Associated Genes: A Comprehensive Analysis and Competitive Endogenous RNA Network Construction

Document Type : Original Articles

Authors

1 Department of Bioinformatics Stella Maris College, Chennai, Tamil Nadu, India

2 Department of Bioinformatics, Stella Maris College, Chennai, Tamil Nadu, India

3 Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, 641021, Tamil Nadu, India

4 Molecular Biology Department, Ampath Lab, Hyderabad, Telangana

10.32592/ARI.2025.80.2.447

Abstract

Breast cancer is a cancer affecting women in which cells become abnormal and multiplies in an uncontrollable fashion. These cancers are hereditary and gene mutations with geographic indications stand alone in most invasive breast cancer types, several other factors like age, gender, ethnic background and environment also contribute for the occurrence. Non-coding RNAs are competing endogenous RNAs that participate in the progression of different cancers. The present study intends to uncover the differentially expression genes in breast cancer. In this study, with the Breast cancer RNA-Seq data obtained from TCGA, expression and survival analyses were performed in order to study gene expression of the samples and genes computationally through R programming. The results obtained after each analysis were inferred visually and logically. Total 613 genes were found to be differentially expressed among the samples out of which 254 were up regulated and 359 were down regulated. The differentially expressed genes obtained using the package TCGA bio links was further used in the construction of ceRNA network. From the results of analyses using TCGA bio links, 352 lncRNAs, 183 miRNAs and 254 mRNAs were found to show aberrant expression in the breast cancer samples. Out of the 352 lncRNAs, the 2 most commonly and repeatedly expressed lncRNAs LINC00 461 and MALAT 1 were found to be more potent therapeutic biomarker and found that their regulated miRNA target genes are enriched in the samples. This study constructed the competing endogenous RNA networks and furthermore unravels the underlying biomarkers for breast cancer cohorts.

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Main Subjects

References

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Archives of Razi Institute
Volume 80, Issue 2
March and April 2025
Pages 447-460

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