Sample-Specific Perturbation of Gene Interactions Identifies Pancreatic Cancer Subtypes
Abstract
:1. Introduction
2. Results
2.1. The Constructed Networks
2.2. Stable Gene–Gene Interaction Network in Normal Pancreatic Tissues
2.3. Network-Based Subtypes
2.4. Heterogeneity among Network-Based Subtypes
2.4.1. Prognosis
2.4.2. Phenotypic Heterogeneity
2.4.3. Gene Mutation and Immune Cell Infiltration
2.4.4. Predictive Therapeutic Efficacy
2.5. Connection with Other Molecular Subtypes of Pancreatic Cancer
2.6. Subtype-3 Specific Pathways and Feature Genes
3. Discussion
4. Materials and Methods
4.1. Data Processing
4.2. Constructing Background Network
4.3. Overview of the Edge-Perturbation-Based Approach
4.4. Construction of the Network-Based Subtypes
4.5. Estimation of the Abundance of Immune Cell Populations
4.6. Chemotherapy Response and Immune Checkpoint Inhibitor Treatment Response Prediction
4.7. Identifying Subtype-Specific Pathways
4.8. Survival Analysis
4.9. Statistical Analysis
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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Wei, R.; Zhang, H.; Cao, J.; Qin, D.; Li, S.; Deng, W. Sample-Specific Perturbation of Gene Interactions Identifies Pancreatic Cancer Subtypes. Int. J. Mol. Sci. 2022, 23, 4792. https://doi.org/10.3390/ijms23094792
Wei R, Zhang H, Cao J, Qin D, Li S, Deng W. Sample-Specific Perturbation of Gene Interactions Identifies Pancreatic Cancer Subtypes. International Journal of Molecular Sciences. 2022; 23(9):4792. https://doi.org/10.3390/ijms23094792
Chicago/Turabian StyleWei, Ran, Huihui Zhang, Jianzhong Cao, Dailei Qin, Shengping Li, and Wuguo Deng. 2022. "Sample-Specific Perturbation of Gene Interactions Identifies Pancreatic Cancer Subtypes" International Journal of Molecular Sciences 23, no. 9: 4792. https://doi.org/10.3390/ijms23094792