Identification of differentially expressed genes between triple and non-triple-negative breast cancer using bioinformatics analysis

  • Qixi Zhai
  • Hao Li
  • Liping Sun
  • Yuan YuanEmail author
  • Xuemei WangEmail author
Original Article



Triple-negative breast cancer (TNBC), defined by lack of expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2), is characterized by early recurrence of disease and poor survival.


Here, we sought to identify genes associated with TNBC that could provide new insight into gene dysregulation in TNBC and, at the same time, provide additional potential therapeutic targets for breast cancer treatment.


Gene expression profiles from accession series GSE76275 were downloaded from the Gene Expression Omnibus database (GEO). The Cancer Genome Atlas (TCGA) was used to validate potential hub genes in the TCGA database. Protein–protein interaction (PPI) networks were identified using STRING (Search Tool for the Retrieval of Interacting Genes/Proteins). Finally, overall survival (OS) and relapse-free survival (RFS) analysis of hub genes was performed using a Kaplan–Meier plotter online tool.


A total of 750 genes were identified after analysis of GSE76275. After validation with the TCGA database, a total of 155 differentially expressed genes (DEGs) were consistent with those identified by GSE76275. Based on the STRING database, we constructed a PPI network using the DEGs obtained from GSE76275 datasets. Furthermore, in the prognostic analysis of the 155 DEGs, we found that there were 10 genes associated with OS and 33 genes associated with RFS. Combined with the degree scores from the PPI network, a total of ten genes with the highest degree scores were selected as hub genes pertaining to TNBC.


Our research provides new insight into the subnetwork of biomarkers connected with TNBC, which could be useful for prognostication and risk stratification of TNBC patients.


Triple-negative breast cancer Differentially expressed genes Protein–protein Interaction Kaplan–Meier plotter 



Triple-negative breast cancer


Estrogen receptor


Progesterone receptor


Human epidermal growth factor receptor 2


Differentially expressed genes


Gene expression omnibus


Protein–protein interaction


The Cancer genome atlas


Overall survival


Relapse-free survival


Log fold control


Epidermal growth factor receptor


Keratin 16


Ret proto-oncogene


Sex-determining region Y-box 1


PDZ domain-containing 1


X-box binding protein 1


Trefoil factor 3


Prostaglandin E receptor 3


NME/NM23 family member 5


Interleukin 6 signal transducer


Author contributions

Conceived and designed the experiments and revised the manuscript: XMW, YY. Performed the experiments: QXZ, LPS, HL. Analyzed the data: QXZ, HL. Responsible for bioinformatics and bio-statistics analysis: QXZ, HL. Wrote the paper: QXZ.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.


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Copyright information

© The Japanese Breast Cancer Society 2019

Authors and Affiliations

  1. 1.Department of Ultrasoundthe First Hospital of China Medical UniversityShenyangChina
  2. 2.Tumor Etiology and Screening Department of Cancer Institute and General Surgerythe First Hospital of China Medical UniversityShenyangChina
  3. 3.Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Departmentthe First Hospital of China Medical UniversityShenyangChina

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