Identifying Tumor-Associated Genes from Bilayer Networks of DNA Methylation Sites and RNAs
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Collection and Preprocessing
2.2. Network Construction
2.2.1. Construction of the DNA Methylation and RNA Interaction Networks
2.2.2. Construction of Bilayer Network of DNA Methylation Sites–RNAs
2.3. Network Indicators
2.3.1. Degree Centrality (DC)
2.3.2. Betweenness Centrality (BC)
2.3.3. Average Degree
2.3.4. ER Random Network
2.3.5. Clustering Coefficient
2.3.6. Shortest Path Length
2.4. Statistical Analysis
2.4.1. Chi-Squared Test
2.4.2. Log Rank Test
2.5. Identification of Differentially Expressed Genes (DEGs)
2.6. Survival Analysis
2.7. KEGG Pathway Enrichment Analysis
3. Results
3.1. Characteristics of DNA Methylation Sites–RNAs Bilayer Network
3.2. Correlation of Hubs with Tumor Development Process
3.3. Correlations between DNA Methylation Sites Located on the Same Gene
3.4. Hubs in DNA Methylation Layer Aggregates Differentially Expressed Genes
3.5. KEGG Pathway Analysis
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Tumor Type | Number of Nodes in the DNA Methylation Layer | Number of Edges in the DNA Methylation Layer | Average Degree | Average Clustering | Average Clustering of the ER Network | Average Path Length | Average Path Length of the ER Network |
---|---|---|---|---|---|---|---|
LUSC | 66,291 | 640,801 | 19.333 | 0.451 | 0.003 | 8.131 | 11.102 |
BRCA | 43,515 | 289,859 | 13.322 | 0.436 | 0.003 | 6.227 | 10.681 |
UCEC | 40,562 | 74,230 | 3.660 | 0.495 | 0.001 | 4.559 | 10.611 |
KIRC | 33,910 | 137,679 | 8.120 | 0.430 | 0.002 | 6.907 | 10.431 |
BLCA | 32,355 | 148,856 | 9.201 | 0.466 | 0.002 | 5.596 | 10.385 |
Degree | Betweenness | |||
---|---|---|---|---|
Tumor Type | Hub DNA Methylation Sites | Corresponding Gene | Hub DNA Methylation Sites | Corresponding Gene |
LUSC | Cg25080152 | MYC | Cg08133058 | SASH1 |
BRCA | Cg24771570 | GRB2 | Cg26383454 | SMIM13 |
UCEC | Cg14751398 | E2F3 | Cg18776056 | FKBP4 |
KIRC | Cg08311343 | CDK6 | Cg19858017 | CLSTN1 |
BLCA | Cg12931157 | NFYA | Cg01473187 | TSPAN6 |
Degree | Betweenness | |||
---|---|---|---|---|
Tumor Type | Single Network | Bilayer Network | Single Network | Bilayer Network |
LUSC | 55 | 100 | 60 | 100 |
BRCA | 51 | 100 | 51 | 100 |
UCEC | 70 | 100 | 63 | 100 |
KIRC | 63 | 100 | 59 | 100 |
BLCA | 54 | 100 | 54 | 100 |
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Xu, X.-J.; Gao, H.-X.; Zhu, L.-C.; Zhu, R. Identifying Tumor-Associated Genes from Bilayer Networks of DNA Methylation Sites and RNAs. Life 2023, 13, 76. https://doi.org/10.3390/life13010076
Xu X-J, Gao H-X, Zhu L-C, Zhu R. Identifying Tumor-Associated Genes from Bilayer Networks of DNA Methylation Sites and RNAs. Life. 2023; 13(1):76. https://doi.org/10.3390/life13010076
Chicago/Turabian StyleXu, Xin-Jian, Hong-Xiang Gao, Liu-Cun Zhu, and Rui Zhu. 2023. "Identifying Tumor-Associated Genes from Bilayer Networks of DNA Methylation Sites and RNAs" Life 13, no. 1: 76. https://doi.org/10.3390/life13010076