Molecular Subtypes and Biomarkers of Ulcerative Colitis Revealed by Sphingolipid Metabolism-Related Genes: Insights from Machine Learning and Molecular Dynamics
Abstract
1. Introduction
2. Methods
2.1. Raw Data Sources
2.2. Integrated Analysis of UC-Related SMGs
2.3. Functional Enrichment Analysis
2.4. Identification of Sphingolipid Metabolism-Related Molecular Subtypes in Patients with UC
2.5. Identifying the Best Model Genes of UC-Related SMGs
2.6. Gene Set Variation Analysis (GSVA) and Immunoinfiltration Analysis
2.7. Cell Culture and Quantitative Real-Time PCR Analysis
2.8. Prediction of Core Gene Transcription Factors (TFs), Cell Localization, and Single-Cell Profiling Analysis
2.9. Prediction of Potential Therapeutic Drugs for UC
3. Results
3.1. Identification of DEGs Associated with UC and SMGs
3.2. Identification of SMG-Related Clusters in UC
3.3. Construction of the Diagnostic Model for UC
3.4. Evaluation of the Diagnostic Model
3.5. Analysis of the Functional Enrichment and Immune Infiltration of the Model Genes
3.6. Screening of Transcription Factor (TFs) of Model Genes and Single-Cell Expression Analysis
3.7. Screening of Potential Therapeutic Agents
4. Discussion
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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Pert_Iname | Moa | Target_Name | Norm_Cs | Free Binding Energy (Kcal/Mol) | ||
---|---|---|---|---|---|---|
CAV1 | PPARG | SLC30A10 | ||||
vemurafenib | RAF inhibitor | BRAF|CYP2C19|CYP3A4|CYP3A5|RAF1 | −1.9033 | −7 | −8.7 | −8 |
NVP-TAE226 | Protein tyrosine kinase inhibitor | IGF1R|PTK2 | −1.7499 | −6.2 | −8.7 | −9.1 |
PD-160170 | Neuropeptide receptor antagonist | NPY1R | −1.7369 | −5.9 | −7.8 | −7.5 |
U-0126 | MEK inhibitor | MAP2K1|MAP2K2|JAK2|AKT1|CHEK1|GSK3B|LCK|MAP2K7|MAPK1|MAPK11|MAPK12|MAPK14|MAPK8|PRKCA|RAF1|ROCK1|RPS6KB1|SGK1 | −1.733 | −6.2 | −7.3 | −6.9 |
selumetinib | MEK inhibitor | MAP2K1|MAP2K2 | −1.7202 | −4.9 | −7.1 | −7.1 |
amperozide | Dopamine receptor antagonist | HTR2A|DRD2|FAAH | −1.7026 | −7 | −8 | −7.4 |
PD-158780 | EGFR inhibitor | EGFR | −1.6983 | −5.4 | −8.2 | −6.8 |
UNC-0321 | Histone lysine methyltransferase inhibitor | EHMT2 | −1.6751 | −5.4 | −7.8 | −7 |
mebendazole | Tubulin inhibitor | TUBA1A|TUBB|TUBB4B | −1.674 | −6.8 | −8.9 | −8 |
PP-2 | Src inhibitor | SRC|LCK|ABL1|LYN|RIPK2 | −1.6735 | −5.3 | −8 | −7.2 |
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Li, Q.; Li, J.; Liu, S.; Zhang, Y.; Liu, J.; Wan, X.; Liang, G. Molecular Subtypes and Biomarkers of Ulcerative Colitis Revealed by Sphingolipid Metabolism-Related Genes: Insights from Machine Learning and Molecular Dynamics. Curr. Issues Mol. Biol. 2025, 47, 616. https://doi.org/10.3390/cimb47080616
Li Q, Li J, Liu S, Zhang Y, Liu J, Wan X, Liang G. Molecular Subtypes and Biomarkers of Ulcerative Colitis Revealed by Sphingolipid Metabolism-Related Genes: Insights from Machine Learning and Molecular Dynamics. Current Issues in Molecular Biology. 2025; 47(8):616. https://doi.org/10.3390/cimb47080616
Chicago/Turabian StyleLi, Quanwei, Junchen Li, Shuyuan Liu, Yunshu Zhang, Jifeng Liu, Xing Wan, and Guogang Liang. 2025. "Molecular Subtypes and Biomarkers of Ulcerative Colitis Revealed by Sphingolipid Metabolism-Related Genes: Insights from Machine Learning and Molecular Dynamics" Current Issues in Molecular Biology 47, no. 8: 616. https://doi.org/10.3390/cimb47080616
APA StyleLi, Q., Li, J., Liu, S., Zhang, Y., Liu, J., Wan, X., & Liang, G. (2025). Molecular Subtypes and Biomarkers of Ulcerative Colitis Revealed by Sphingolipid Metabolism-Related Genes: Insights from Machine Learning and Molecular Dynamics. Current Issues in Molecular Biology, 47(8), 616. https://doi.org/10.3390/cimb47080616