Genome-Wide Investigation of Genes Regulated by ERα in Breast Cancer Cells
Abstract
:1. Introduction
2. Results
2.1. Identification of DEGs between ERα Transgenic MDA-MB-231 and Wild Type MDA-MB-231 Cells
2.2. Validation of Gene Expression Data by Real-Time PCR
2.3. GO Enrichment of DEGs
2.4. Pathway Analysis of DEGs
2.5. PPI Network Analysis
2.6. Comparison of the DEGs Identified in ERα Transgenic MDA-MB-231 versus E2 Stimulated MCF-7 Cells
2.7. Bioinformatics Analysis of Common Genes Detected in ERα Transgenic 231 versus E2 Stimulated MCF-7 Cells
3. Discussion
4. Materials and Methods
4.1. Cell Culture
4.2. Construction of ERα Transgenic MDA-MB-231Cell Line
4.3. Western-Blotting
4.4. RNA-Seq Analysis
4.5. Identification of Differentially Expressed Genes (DEGs)
4.6. Validation by RT-PCR
4.7. GO Enrichment and KEGG Pathway Analysis
4.8. Construction of Protein-Protein Interaction (PPI) Networks
4.9. Microarray Data Analysis
4.10. Validation Overlapped Genes by RT-PCT and The Cancer Genome Atlas (TCGA) Analysis
4.11. Verification Genes with ERα Binding Sites
4.12. Identification of DEGs between ER Positive and Negative Breast Cancer Patients
4.13. Kaplan–Meier Plotter Analysis
4.14. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Sample Availability: Samples of the compounds are available from the authors. |
Genes | Gene ID | RNA-Seq | |
---|---|---|---|
Fold Change | Significant | ||
ESR1 | 2099 | 1053 | Up |
PCK2 | 5106 | 2.57 | Up |
CXCL1 | 2919 | 2.29 | Up |
KIF21B | 23046 | 7 | Up |
VCL | 7414 | 6.63 | Up |
FOS | 2353 | 0.02 | Down |
HMOX1 | 3162 | 0.41 | Down |
DUSP1 | 1843 | 0.3 | Down |
ID3 | 3399 | 0.45 | Down |
Genes | RNA-Seq | Microarray Data | Significance | ||
---|---|---|---|---|---|
Fold Change | p-Value | Fold Change | p-Value | ||
SLC1A1 | 1.503 | 0.0406 | 1.878 | 2.18 × 10−6 | up |
RASA1 | 1.71 | 0.000281 | 1.879 | 2.89 × 10−6 | up |
SP1 | 1.603 | 0.005176 | 1.801 | 6.38 × 10−6 | up |
ABAT | 2.545 | 0.005576 | 1.857 | 4.42 × 10−8 | up |
TNFRSF12A | 0.67 | 0.0029 | 0.65 | 1.84 × 10−5 | down |
ID3 | 0.446 | 3.05 × 10−08 | 0.5 | 8.36 × 10−8 | down |
BAMBI | 0.42 | 7.05 × 10−07 | 0.491 | 1.65 × 10−8 | down |
JUNB | 0.65 | 0.003262 | 0.55 | 5.20 × 10−7 | down |
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Wang, S.; Li, X.; Zhang, W.; Gao, Y.; Zhang, K.; Hao, Q.; Li, W.; Wang, Z.; Li, M.; Zhang, W.; et al. Genome-Wide Investigation of Genes Regulated by ERα in Breast Cancer Cells. Molecules 2018, 23, 2543. https://doi.org/10.3390/molecules23102543
Wang S, Li X, Zhang W, Gao Y, Zhang K, Hao Q, Li W, Wang Z, Li M, Zhang W, et al. Genome-Wide Investigation of Genes Regulated by ERα in Breast Cancer Cells. Molecules. 2018; 23(10):2543. https://doi.org/10.3390/molecules23102543
Chicago/Turabian StyleWang, Shuning, Xiaoju Li, Wangqian Zhang, Yuan Gao, Kuo Zhang, Qiang Hao, Weina Li, Zhaowei Wang, Meng Li, Wei Zhang, and et al. 2018. "Genome-Wide Investigation of Genes Regulated by ERα in Breast Cancer Cells" Molecules 23, no. 10: 2543. https://doi.org/10.3390/molecules23102543