Evaluation and Comparison of Multi-Omics Data Integration Methods for Subtyping of Cutaneous Melanoma
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Preprocessing and Analysis
2.2. RNA-Seq Data Preprocessing
2.3. Joint Singular Value Decomposition
2.4. Performance Evaluation
2.5. Feature Analysis
2.6. Skin Cutaneous Melanoma Molecular and Clinical Features
3. Results
3.1. Data Fusion
3.2. Feature Extraction
3.3. Survival
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Genomic Domain/DF Method | Mutation Subtypes (TCGA) | RNA-seq Cluster Consenhier (TCGA) | Methylation Types 2014 08 (TCGA) | Silhouette Score |
---|---|---|---|---|
RNA-seq | −0.014 | 0.287 | 0.117 | 0.07, 0.135, 0.018, 0.037 |
Methylation | 0.004 | 0.061 | 0.514 | 0.025, 0.026, 0.058 |
Spectrum | 0.039 | 0.128 | 0.38 | 0.024, 0.03, 0.026 |
SNF | 0.027 | 0.152 | 0.275 | 0.008, 0.004, 0.004 |
NEMO | 0.029 | 0.108 | 0.195 | 0.05, −0.017, −0.015, −0.03, −0.008, 0.005, 0.031, −0.014, −0.027, −0.019, −0.023, −0.009 |
jSVD | 0 | 0.272 | 0.147 | 0.212, 0.339, 0.281 |
Mutation subtypes (TCGA) | 1 | 0.007 | 0.021 | NA |
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Amaro, A.; Pfeffer, M.; Pfeffer, U.; Reggiani, F. Evaluation and Comparison of Multi-Omics Data Integration Methods for Subtyping of Cutaneous Melanoma. Biomedicines 2022, 10, 3240. https://doi.org/10.3390/biomedicines10123240
Amaro A, Pfeffer M, Pfeffer U, Reggiani F. Evaluation and Comparison of Multi-Omics Data Integration Methods for Subtyping of Cutaneous Melanoma. Biomedicines. 2022; 10(12):3240. https://doi.org/10.3390/biomedicines10123240
Chicago/Turabian StyleAmaro, Adriana, Max Pfeffer, Ulrich Pfeffer, and Francesco Reggiani. 2022. "Evaluation and Comparison of Multi-Omics Data Integration Methods for Subtyping of Cutaneous Melanoma" Biomedicines 10, no. 12: 3240. https://doi.org/10.3390/biomedicines10123240