Systematic Comparison of CRISPR and shRNA Screens to Identify Essential Genes Using a Graph-Based Unsupervised Learning Model
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Description
2.2. Overall Description of Our Workflow
2.3. Graph-Based Unsupervised Learning Model
2.4. Iterative Updating to Obtain Common Essential Genes
2.5. The Final Essential Genes for Each Cell Line Were Obtained
2.6. Statistical Analysis of shRNA- and CRISPR-Based Essential Genes with Different Expression Levels
3. Results
3.1. Graph-Based Machine Learning Models Converge on Both shRNAs and CRIPSRs with the Same Trends
3.2. Not a Single Gene Is Essential in All Cancer Cell Lines
3.3. Gene Expression and Gene Essentiality Are Positively Correlated According to Both shRNA and CRISPR Screening Methodologies
3.4. shRNA Outperforms CRISPR in the Identification of Essential Genes with Low Expression Levels
3.5. Most Essential Genes Are Highly Expressed, and CRISPR Has a Slightly Better Ability to Identify Highly Expressed Essential Genes
3.6. The Essential Genes Identified via shRNA and CRISPR Have Little Overlap, and Most of the Genes Expressed at Low Levels can Be Identified Only by shRNA
4. Conclusions and Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Ding, Y.; Denomy, C.; Freywald, A.; Pan, Y.; Vizeacoumar, F.J.; Vizeacoumar, F.S.; Wu, F.-X. Systematic Comparison of CRISPR and shRNA Screens to Identify Essential Genes Using a Graph-Based Unsupervised Learning Model. Cells 2024, 13, 1653. https://doi.org/10.3390/cells13191653
Ding Y, Denomy C, Freywald A, Pan Y, Vizeacoumar FJ, Vizeacoumar FS, Wu F-X. Systematic Comparison of CRISPR and shRNA Screens to Identify Essential Genes Using a Graph-Based Unsupervised Learning Model. Cells. 2024; 13(19):1653. https://doi.org/10.3390/cells13191653
Chicago/Turabian StyleDing, Yulian, Connor Denomy, Andrew Freywald, Yi Pan, Franco J. Vizeacoumar, Frederick S. Vizeacoumar, and Fang-Xiang Wu. 2024. "Systematic Comparison of CRISPR and shRNA Screens to Identify Essential Genes Using a Graph-Based Unsupervised Learning Model" Cells 13, no. 19: 1653. https://doi.org/10.3390/cells13191653
APA StyleDing, Y., Denomy, C., Freywald, A., Pan, Y., Vizeacoumar, F. J., Vizeacoumar, F. S., & Wu, F.-X. (2024). Systematic Comparison of CRISPR and shRNA Screens to Identify Essential Genes Using a Graph-Based Unsupervised Learning Model. Cells, 13(19), 1653. https://doi.org/10.3390/cells13191653