Multi-Omics Analysis of SOX4, SOX11, and SOX12 Expression and the Associated Pathways in Human Cancers
Abstract
:1. Introduction
2. Results
2.1. mRNA Expression of the SOX Gene Family in Various Cancers
2.2. SOX4 Expression and Its Prognostic Value in Various Cancers
2.3. SOX11 Expression Pattern and Patient Survival in Various Cancers
2.4. SOX12 Expression Pattern and Patient Survival in Various Cancers
2.5. Clinical Prognosis of the Three SOX Genes in Liver Cancer
2.6. Clinical Prognosis of the Three SOX Genes in Sarcoma
2.7. Functional Protein Partners and Their Predicted Signaling Pathways
3. Discussion
4. Materials and Methods
4.1. Oncomine Database Analysis
4.2. Molecular Evolutionary Genetics Analysis
4.3. GEPIA2 Database Analysis
4.4. cBioPortal Database Analysis
4.5. Kaplan–Meier Plotter
4.6. R2: Genomic Analysis and Visualization Platform
4.7. Gene Correlation Analysis of SOX4, SOX11, and SOX12
4.8. Identification of Functional Protein Partners of SOX4, SOX11, and SOX12, and Signaling Pathway Analysis
4.9. Analysis of SOX Protein Expression Pattern in Various Types of Cancer
4.10. Analysis of Gene Network with SOX4, SOX11, and SOX12
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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#Term ID | Term Description | False Discovery Rate |
---|---|---|
hsa05213 | Endometrial cancer | 2.20 × 10−20 |
hsa05215 | Prostate cancer | 4.75 × 10−18 |
hsa05200 | Pathways in cancer | 2.24 × 10−17 |
hsa04310 | Wnt signaling pathway | 2.61 × 10−16 |
hsa05226 | Gastric cancer | 2.92 × 10−16 |
hsa04520 | Adherens junction | 3.34 × 10−16 |
hsa05225 | Hepatocellular carcinoma | 7.38 × 10−16 |
hsa05165 | Human papillomavirus infection | 2.76 × 10−15 |
hsa05217 | Basal cell carcinoma | 5.93 × 10−15 |
hsa05206 | MicroRNAs in cancer | 8.70 × 10−15 |
hsa04390 | Hippo signaling pathway | 9.90 × 10−15 |
hsa05210 | Colorectal cancer | 6.99 × 10−14 |
hsa05224 | Breast cancer | 2.64 × 10−13 |
hsa04934 | Cushing’s syndrome | 3.71 × 10−13 |
hsa05216 | Thyroid cancer | 4.14 × 10−13 |
hsa04115 | p53 signaling pathway | 4.94 × 10−13 |
hsa04110 | Cell cycle | 1.55 × 10−12 |
hsa05166 | HTLV-I infection | 4.71 × 10−11 |
hsa04916 | Melanogenesis | 4.15 × 10−10 |
hsa04218 | Cellular senescence | 4.27 × 10−10 |
#Term ID | Term Description | False Discovery Rate |
---|---|---|
HSA-201681 | TCF-dependent signaling in response to WNT | 4.69 × 10−15 |
HSA-3769402 | Deactivation of the β-catenin transactivating complex | 4.69 × 10−15 |
HSA-8878159 | Transcriptional regulation by RUNX3 | 1.63 × 10−12 |
HSA-212436 | Generic Transcription Pathway | 3.64 × 10−12 |
HSA-2990846 | SUMOylation | 5.69 × 10−12 |
HSA-74160 | Gene expression (Transcription) | 9.40 × 10−12 |
HSA-195253 | Degradation of β-catenin by the destruction complex | 1.42 × 10−11 |
HSA-162582 | Signal Transduction | 3.63 × 10−11 |
HSA-1640170 | Cell Cycle | 4.88 × 10−11 |
HSA-201722 | Formation of the β-catenin/TCF transactivating complex | 7.06 × 10−11 |
HSA-6804760 | Regulation of TP53 activity through methylation | 4.81 × 10−10 |
HSA-3065678 | SUMO is transferred from E1 to E2 (UBE2I, UBC9) | 6.14 × 10−10 |
HSA-4411364 | Binding of TCF/LEF: CTNNB1 to target gene promoters | 1.59 × 10−9 |
HSA-8951430 | RUNX3 regulates WNT signaling | 1.59 × 10−9 |
HSA-3108232 | SUMO E3 ligases SUMOylate target proteins | 1.86 × 10−9 |
HSA-69563 | p53-dependent G1 DNA Damage Response | 3.53 × 10−9 |
HSA-1643685 | Disease | 4.70 × 10−9 |
HSA-3700989 | Transcriptional Regulation by TP53 | 6.39 × 10−9 |
HSA-5663202 | Diseases of signal transduction | 6.39 × 10−9 |
HSA-6804757 | Regulation of TP53 Degradation | 6.39 × 10−9 |
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Seok, J.; Gil, M.; Dayem, A.A.; Saha, S.K.; Cho, S.-G. Multi-Omics Analysis of SOX4, SOX11, and SOX12 Expression and the Associated Pathways in Human Cancers. J. Pers. Med. 2021, 11, 823. https://doi.org/10.3390/jpm11080823
Seok J, Gil M, Dayem AA, Saha SK, Cho S-G. Multi-Omics Analysis of SOX4, SOX11, and SOX12 Expression and the Associated Pathways in Human Cancers. Journal of Personalized Medicine. 2021; 11(8):823. https://doi.org/10.3390/jpm11080823
Chicago/Turabian StyleSeok, Jaekwon, Minchan Gil, Ahmed Abdal Dayem, Subbroto Kumar Saha, and Ssang-Goo Cho. 2021. "Multi-Omics Analysis of SOX4, SOX11, and SOX12 Expression and the Associated Pathways in Human Cancers" Journal of Personalized Medicine 11, no. 8: 823. https://doi.org/10.3390/jpm11080823