Inquiry Regarding Unexpected Results in Gene Knockout Experiment Using GenKI Algorithm

[linWiky]

Dear GenKI Development Team,

I hope this message finds you well.

First and foremost, I would like to express my gratitude for the development of the GenKI algorithm, which is an outstanding and innovative tool for gene knockout experiments. It has provided great support for my research and has been an invaluable asset in advancing our work.

However, I have encountered some perplexing results while using the GenKI algorithm to conduct multi-gene random knockout experiments, and I would like to seek your advice.

During the analysis of my data, where I performed random knockouts of multiple genes, I observed that, apart from the target gene itself, there were almost no significant perturbations in related genes. More concerning, many genes did not show any changes in their own expression after being knocked out. This lack of perturbation in gene expression seems unusual, and I am unsure whether this is expected behavior of the algorithm or if there is an issue with my data or approach.

To help clarify this matter, I have attached a screenshot of the experiment results and the relevant outputs. Could you please confirm whether this phenomenon is expected when using the GenKI algorithm? If there are any potential reasons for this or suggestions for improving the analysis, I would greatly appreciate your guidance.

I look forward to your response and thank you for your hard work and valuable contributions to the scientific community.

Best regards

[linWiky]

[linWiky]