Comparison Bioinformatic Analysis of Extracellular Vesicles-Related Genes and MicroRNAs in Breast Cancer
Abstract
1. Introduction
2. Results
2.1. Expression Profile Results
2.2. Gene Correlation and Targeted Expression Analysis Results
2.3. The Promotor Methylation Analysis
2.4. The Overall Survival Status
2.5. The Relationship Between MicroRNA vs. BC and MicroRNA vs. RNA
2.6. Gene Set Enrichment Analysis of ENPEP, TIMP1, CD36, MARCKS, DAB2, and CXCL14
2.7. Tumor, Normal, and Metastatic (TNM) Analysis
2.8. Cancer Hallmark Enrichment Analysis
2.9. Result of miRNAs Associated with Genes
2.10. Gene–Gene Interaction
3. Discussion
Limitation
4. Materials and Methods
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
Abbreviation | Full Name |
BC | Breast cancer |
EV | Extracellular vesicle |
miRNA | MicroRNA |
lncRNA | Long non-coding RNA |
IHC | Immunohistochemistry |
OS | Overall survival |
GEPIA2 | Gene Expression Profiling Interactive Analysis 2 |
HPA | Human Protein Atlas |
UALCAN | University of Alabama at Birmingham CANcer data analysis portal |
TNM | Tumor, Normal, and Metastatic |
KM Plotter | Kaplan–Meier Plotter |
ENCORI | Encyclopedia of RNA Interactomes |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
GO | Gene Ontology |
STRING | Search Tool for the Retrieval of Interacting Genes/Proteins |
PAM50 | Prediction Analysis of Microarray 50 |
TNBC | Triple negative breast cancer |
ER | Estrogen receptor |
PR | Progesterone receptor |
HER2 | Human Epidermal Growth Factor Receptor 2 |
TIMP1 | Tissue inhibitor of metalloproteinases 1 |
CD36 | Cluster of Differentiation 36 |
MARCKS | Myristoylated Alanine-Rich C Kinase Substrate |
DAB2 | Disabled Homolog 2 |
CXCL14 | C-X-C Motif Chemokine Ligand 14 |
ENPEP | Glutamyl Aminopeptidase |
miR-181b-5p | MicroRNA-181b-5p |
miR-222-3p | MicroRNA-222-3p |
miRDB | MicroRNA Target Prediction Database |
TargetScan | TargetScan microRNA target prediction tool |
TCGA | The Cancer Genome Atlas |
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Cancer Hallmark | Overlap | p-Value | Adjusted p-Value | Odds Ratio | Hallmark vs. Hallmark | Genes |
---|---|---|---|---|---|---|
Sustaining Proliferative Signaling | 4/3574 | 0.03172 | 0.06175 | 5.76 | 0.69 | TIMP1; ENPEP; CD36; CXCL14 |
Genome Instability | 0/1 | nan | 1.0 | nan | 0.0 | nan |
Evading Growth Suppressors | 5/3288 | 0.00248 | 0.01012 | 13.08 | 0.93 | TIMP1; CXCL14; DAB2; ENPEP; MARCKS |
Evading Immune Destruction | 1/749 | 0.26464 | 0.26464 | 5.19 | 0.82 | CXCL14 |
Sustained Angiogenesis | 3/796 | 0.00264 | 0.01012 | 17.9 | 2.31 | TIMP1; CD36; CXCL14 |
Tissue Invasion and Metastasis | 3/2318 | 0.05115 | 0.07672 | 5.48 | 0.79 | TIMP1; ENPEP; CD36 |
Tumor-Promoting Inflammation | 2/769 | 0.03431 | 0.06175 | 10.3 | 1.6 | CD36; CXCL14 |
Resisting Cell Death | 4/1941 | 0.00337 | 0.01012 | 12.13 | 1.26 | TIMP1; DAB2; CD36; CXCL14 |
Reprogramming Energy Metabolism | 1/740 | 0.26185 | 0.26464 | 5.26 | 0.83 | CD36 |
Replicative Immortality | 1/547 | 0.19983 | 0.25692 | 7.21 | 1.12 | CXCL14 |
Gene Groups | miRNAs Related to Genes |
---|---|
CD36 and DAB2 | hsa-miR-4729, hsa-miR-651-5p, hsa-miR-5579-3p, hsa-miR-4520-2-3p |
DAB2 and CXCL14 | hsa-miR-4713-5p, hsa-miR-548t-5p, hsa-miR-548az-5p |
CD36 and CXCL14 | hsa-miR-4719, hsa-miR-340-5p, hsa-miR-651-3p, hsa-miR-4477b, hsa-miR-1277-5p, hsa-miR-150-5p, hsa-miR-153-5p, hsa-miR-6854-5p, hsa-miR-548ar-3p, hsa-miR-548a-3p, hsa-miR-548f-3p, hsa-miR-548az-3p, hsa-miR-548e-3p |
MARCKS and CXCL14 | hsa-miR-3121-5p, hsa-miR-5088-3p, hsa-miR-3143 |
ENPEP and CXCL14 | hsa-miR-3163, hsa-miR-3662, hsa-miR-106a-3p, hsa-miR-142-5p, hsa-miR-5590-3p |
ENPEP and CD36 | hsa-miR-548e-5p, hsa-miR-4659a-3p, hsa-miR-4659b-3p |
CD36 and MARCKS | hsa-miR-1537-5p, hsa-miR-4276, hsa-miR-545-3p, hsa-miR-134-3p, hsa-miR-3124-3p, hsa-miR-655-3p, hsa-miR-374c-5p, hsa-miR-576-5p |
ENPEP and MARCKS | hsa-miR-9-5p, hsa-miR-641, hsa-miR-3617-5p, hsa-miR-520d-5p, hsa-miR-524-5p, hsa-miR-551b-5p, hsa-miR-4668-3p, hsa-miR-3606-3p, hsa-miR-513a-3p, hsa-miR-513c-3p, hsa-miR-4490 |
MARCKS and DAB2 | hsa-miR-6878-5p, hsa-miR-6825-5p, hsa-miR-664b-3p, hsa-miR-579-3p, hsa-miR-3925-3p, hsa-let-7c-3p |
ENPEP and DAB2 | hsa-miR-1297, hsa-miR-26a-5p, hsa-miR-26b-5p, hsa-miR-4465, hsa-miR-376a-5p, hsa-miR-3150b-3p, hsa-miR-4784, hsa-miR-3977, hsa-miR-6768-3p, hsa-miR-15b-3p, hsa-miR-4428 |
ENPEP and DAB2 and CXCL14 | hsa-miR-186-5p, hsa-miR-320d, hsa-miR-320c, hsa-miR-320b, hsa-miR-4429, hsa-miR-9-3p |
CD36 and MARCKS and DAB2 | hsa-miR-5696 |
CD36, MARCKS and CXCL14 | hsa-miR-410-3p |
CD36, DAB2 and CXCL14 | hsa-miR-539-5p, hsa-miR-526b-3p, hsa-miR-93-5p, hsa-miR-20b-5p, hsa-miR-106b-5p, hsa-miR-20a-5p, hsa-miR-17-5p, hsa-miR-519d-3p, hsa-miR-106a-5p |
ENPEP, CD36 and MARCKS | hsa-miR-4328, hsa-miR-548c-3p |
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Ayan, D.; Bozkurt Polat, S.B.; Ozmen, E.; Gul, M.A. Comparison Bioinformatic Analysis of Extracellular Vesicles-Related Genes and MicroRNAs in Breast Cancer. Int. J. Mol. Sci. 2025, 26, 5906. https://doi.org/10.3390/ijms26125906
Ayan D, Bozkurt Polat SB, Ozmen E, Gul MA. Comparison Bioinformatic Analysis of Extracellular Vesicles-Related Genes and MicroRNAs in Breast Cancer. International Journal of Molecular Sciences. 2025; 26(12):5906. https://doi.org/10.3390/ijms26125906
Chicago/Turabian StyleAyan, Durmus, Serife Buket Bozkurt Polat, Esma Ozmen, and Mehmet Ali Gul. 2025. "Comparison Bioinformatic Analysis of Extracellular Vesicles-Related Genes and MicroRNAs in Breast Cancer" International Journal of Molecular Sciences 26, no. 12: 5906. https://doi.org/10.3390/ijms26125906
APA StyleAyan, D., Bozkurt Polat, S. B., Ozmen, E., & Gul, M. A. (2025). Comparison Bioinformatic Analysis of Extracellular Vesicles-Related Genes and MicroRNAs in Breast Cancer. International Journal of Molecular Sciences, 26(12), 5906. https://doi.org/10.3390/ijms26125906