Bioinformatics and Omics-based Perspectives on Breast Cancer: Advancing Target Gene Identification for the Development of Anticancer Agents

Irmasari, Irmasari; Rahmat, Alim Khodimul; Yoga, I Made Bayu Kresna; Maharani, Dini; Widayanti, Wasita Rachma; Widyardhita, Monica Hana; Saputra, Bakti Wahyu; Haidar, Inas; Amalia, Amalia; Ningsih, Sri Rahmayani; Putri, Dyaningtyas Dewi Pamungkas; Hermawan, Adam

doi:10.31557/APJCP.2025.26.7.2291

Bioinformatics and Omics-based Perspectives on Breast Cancer: Advancing Target Gene Identification for the Development of Anticancer Agents

Document Type : Systematic Review and Meta-analysis

Authors

Irmasari Irmasari ¹^{, 2}
Alim Khodimul Rahmat ³
I Made Bayu Kresna Yoga ¹^{, 2}
Dini Maharani ⁴
Wasita Rachma Widayanti ⁴
Monica Hana Widyardhita ⁴
Bakti Wahyu Saputra ¹
Inas Haidar ¹
Amalia Amalia ¹
Sri Rahmayani Ningsih ¹
Dyaningtyas Dewi Pamungkas Putri ²^{, 5}
Adam Hermawan ²^{, 6}

¹ Master’s Student in Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Gadjah Mada, Sekip Utara II, 55281 Yogyakarta, Indonesia.

² Laboratory of Advanced Pharmaceutical Sciences, Faculty of Pharmacy, Gadjah Mada University, Yogyakarta, Indonesia.

³ Doctoral Student in Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Gadjah Mada, Sekip Utara II, 55281 Yogyakarta, Indonesia.

⁴ Undergraduate Student in Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Gadjah Mada, Sekip Utara II, 55281 Yogyakarta, Indonesia.

⁵ Laboratory of Pharmacology and Toxicology, Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281 Yogyakarta, Indonesia.

⁶ Laboratory of Macromolecular Engineering, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281 Yogyakarta, Indonesia.

10.31557/APJCP.2025.26.7.2291

Abstract

Objective: Breast cancer remains the leading cause of mortality among women worldwide. Innovative strategies, particularly bioinformatics and omics-based approaches, play a crucial role in identifying potential target genes for breast cancer treatment. This review aims to highlight the future acceleration of drug discovery from single natural compounds and plant-derived natural products, including Traditional Chinese Medicines (TCMs), and to explore their potential in enhancing the efficacy of conventional drugs when combined, through the application of bioinformatics tools and various omics-based databases, web servers, or software platforms. Methods: This review focuses on research conducted over the past five years, utilizing three major scientific databases: PubMed, ScienceDirect, and Scopus. Using the Rayyan platform, we systematically narrowed 3,800 original studies down to 70 relevant articles. Result: The findings present a comprehensive overview of key bioinformatics approaches and omics-based resources, including databases, web servers, and software tools, covering data mining, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, Protein-Protein Interaction (PPI) network construction and hub gene selection, genetic alteration, and survival analysis. These tools have been employed to identify potential target genes that contribute to the acceleration of drug discovery from single natural compounds and plant-derived natural products, including Traditional Chinese Medicines (TCMs), as well as their role in improving the therapeutic efficacy of conventional drugs when used in combination. Conclusion: A comprehensive understanding of omics-based databases, web servers and software can facilitate the acceleration of new drug discovery and enhance the effectiveness of existing conventional drugs in breast cancer therapy. This approach supports validation in preclinical models, both in vitro and in vivo, ensuring clinical applicability.

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