A Comprehensive and Integrative Approach to MeCP2 Disease Transcriptomics
Abstract
:1. Introduction
2. Results
2.1. Comprehensive Resource of MeCP2 Transcriptomes
2.2. MeCP2 Transcriptomics in Mice Reveal a Common Core of Misregulated Genes
2.3. Cross-Species and Cross-Disease Comparisons of MeCP2′s Transcriptomic Signature
2.4. Sample Size Has a Major Impact on DEG Detection
2.5. Batch and Technical Variation Must Be Overcome in Order to Integrate and Understand Data
3. Discussion
4. Materials and Methods
4.1. Data Collection
4.2. Mouse Data Processing
4.3. Data Annotation
4.4. Data Visualization
4.5. Portal Development
4.6. Core Gene Identification and Clustering
4.7. Core Gene Characteristics and Location
4.8. GO Analysis
4.9. Human Data Processing and Comparative Analysis
4.10. Other Model Data Processing and Comparative Analysis
4.11. GSEA
4.12. ASD Model Comparison
4.13. Down Sampling Analysis
4.14. Technical Variation/Batch Effect Analysis
4.15. Sex Comparison
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Trostle, A.J.; Li, L.; Kim, S.-Y.; Wang, J.; Al-Ouran, R.; Yalamanchili, H.K.; Liu, Z.; Wan, Y.-W. A Comprehensive and Integrative Approach to MeCP2 Disease Transcriptomics. Int. J. Mol. Sci. 2023, 24, 5122. https://doi.org/10.3390/ijms24065122
Trostle AJ, Li L, Kim S-Y, Wang J, Al-Ouran R, Yalamanchili HK, Liu Z, Wan Y-W. A Comprehensive and Integrative Approach to MeCP2 Disease Transcriptomics. International Journal of Molecular Sciences. 2023; 24(6):5122. https://doi.org/10.3390/ijms24065122
Chicago/Turabian StyleTrostle, Alexander J., Lucian Li, Seon-Young Kim, Jiasheng Wang, Rami Al-Ouran, Hari Krishna Yalamanchili, Zhandong Liu, and Ying-Wooi Wan. 2023. "A Comprehensive and Integrative Approach to MeCP2 Disease Transcriptomics" International Journal of Molecular Sciences 24, no. 6: 5122. https://doi.org/10.3390/ijms24065122