Single-Sample Networks Reveal Intra-Cytoband Co-Expression Hotspots in Breast Cancer Subtypes
Abstract
1. Introduction
2. Results
2.1. Aggregated Networks Disruption Across Breast Cancer Subtypes
2.2. Intrachromosomal and Intracytoband Interaction Dynamics in Aggregated Networks
2.3. Breast Cancer Heterogeneity in Genomic Interactions According to Co-Expression Aggregated Networks
2.4. Interaction Patterns in Single-Sample Co-Expression Networks
2.5. Chromosomal and Cytoband Interaction Patterns in Single-Sample Networks
2.6. Single-Sample Network Analysis Reveals Key Topological Differences in Breast Cancer Subtypes
2.7. Comparative Co-Expression Patterns Between Aggregated and Single-Sample Networks
2.8. The Proportion of CIS Interactions Occurring in Single-Sample Co-Expression Networks and Survival Outcomes
2.9. High-Degree Gene Distribution and Cytoband Localization in Single-Sample Networks
3. Discussion
4. Materials and Methods
4.1. Data Acquisition and Pre-Processing
4.2. Gene Co-Expression Network Inference
4.3. Inference of Single-Sample Co-Expression Networks
4.4. Intra-Chromosomal Proportion of Co-Expression Networks
4.5. Survival Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Subtype | Chromosome | Frequency | Proportion |
---|---|---|---|
1 | 223 | 0.000105 | |
Healthy | 19 | 98 | 0.000090 |
2 | 89 | 0.000114 | |
17 | 1742 | 0.002479 | |
Luminal A | 11 | 1601 | 0.001847 |
8 | 871 | 0.003520 | |
11 | 1612 | 0.001860 | |
Luminal B | 17 | 1530 | 0.002177 |
8 | 792 | 0.003201 | |
17 | 2047 | 0.002913 | |
Her2 | 8 | 754 | 0.003047 |
11 | 698 | 0.000805 | |
1 | 1013 | 0.000475 | |
Basal | 19 | 749 | 0.000687 |
10 | 641 | 0.002396 |
Subtype | Cytoband | Frecuency | Proportion |
---|---|---|---|
6p21.32 | 17 | 0.010650 | |
Healthy | 8p11.23 | 13 | 0.068420 |
8q24.3 | 7 | 0.001210 | |
11q13.1 | 264 | 0.051250 | |
Luminal A | 8q24.3 | 206 | 0.035650 |
11q13.2 | 151 | 0.062530 | |
8q24.3 | 377 | 0.065247 | |
Luminal B | 17q11.2 | 227 | 0.066706 |
11q13.1 | 205 | 0.039798 | |
17q11.2 | 367 | 0.107850 | |
Her2 | 8q24.3 | 331 | 0.057290 |
17q25.3 | 325 | 0.061870 | |
6p21.1 | 272 | 0.066420 | |
Basal | 8q24.3 | 224 | 0.038770 |
17q25.3 | 182 | 0.034650 |
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Ponce-Cusi, R.; López-Sánchez, P.; Maracaja-Coutinho, V.; Espinal-Enríquez, J. Single-Sample Networks Reveal Intra-Cytoband Co-Expression Hotspots in Breast Cancer Subtypes. Int. J. Mol. Sci. 2024, 25, 12163. https://doi.org/10.3390/ijms252212163
Ponce-Cusi R, López-Sánchez P, Maracaja-Coutinho V, Espinal-Enríquez J. Single-Sample Networks Reveal Intra-Cytoband Co-Expression Hotspots in Breast Cancer Subtypes. International Journal of Molecular Sciences. 2024; 25(22):12163. https://doi.org/10.3390/ijms252212163
Chicago/Turabian StylePonce-Cusi, Richard, Patricio López-Sánchez, Vinicius Maracaja-Coutinho, and Jesús Espinal-Enríquez. 2024. "Single-Sample Networks Reveal Intra-Cytoband Co-Expression Hotspots in Breast Cancer Subtypes" International Journal of Molecular Sciences 25, no. 22: 12163. https://doi.org/10.3390/ijms252212163
APA StylePonce-Cusi, R., López-Sánchez, P., Maracaja-Coutinho, V., & Espinal-Enríquez, J. (2024). Single-Sample Networks Reveal Intra-Cytoband Co-Expression Hotspots in Breast Cancer Subtypes. International Journal of Molecular Sciences, 25(22), 12163. https://doi.org/10.3390/ijms252212163