Single-Cell Network In Silico Knockout and State Perturbation Analysis
Graphical abstract
Summary
Single-cell state models and network perturbations prioritise intervention hypotheses with explicit robustness checks. The graphical abstract integrates data distributions, model responses and feature comparisons across analytical layers. The results establish clear priorities for features, perturbations or biomarker candidates. The result-focused presentation supports efficient review of the main evidence and research priorities. It also supports focused comparison across the disclosed computational results.
Computational results
Figure 4 In the female stage Target D virtual knockout
a, median log2 of male and female procedural genes at each female stage, and 1+ regulatory effect FC) and elimination of comparison of the neutral genes matching expression rates and network range. a, the median log2 of the male and female procedural genes at each female stage, and 1+ control effects FC), and the comparison of the neutral genes matched by expression rate and network amplitude. b, the middle effects between the seeds of the core sex genes. The error range represents the quadratic spacing of the three random seeds.
This figure presents the principal structures and trends in “Figure 4 In the female stage Target D virtual knockout” and connects them to the case-level ranking and result interpretation.
Figure 5 Men's Stage Target A and Target B Virtual knockout
a, median log2 of the two DNAmt3 side sequences of the same source genes for the female and male processes. a, the median log2 of the two DNAmt3 side-parent homologous genes for the female and the male processes; 1+ regulatory effect FC)•b, the response spectrum of the core sex genes. The effect FC represents the multiple of the flow space distance relative to the background expectations, rather than the expression of the change in the multiple.
This figure presents the principal structures and trends in “Figure 5 Men's Stage Target A and Target B Virtual knockout” and connects them to the case-level ranking and result interpretation.
Figure 6 Specification of the phase of elimination of Target C
a, high-responsiveness gene network effect heatmap at each stage. a, network effect heatmap of high-response genes at each stage. b, gene response correlation of the final female stage to the earliest intercourse stage, used to identify transition response rearrangement.
This figure presents the principal structures and trends in “Figure 6 Specification of the phase of elimination of Target C” and connects them to the case-level ranking and result interpretation.
Figure 7 Related to Rampant Seeds and Negative Contrast
a, overlapping Jaccard collection of different random seed Top50 high-response genes. a, Jackcard overlapping of different random seed Top50 high-response gene sets. b, targeted knockout with matching neutral gene knockouts in the FDR<0.05 gene ratio.
This figure presents the principal structures and trends in “Figure 7 Related to Rampant Seeds and Negative Contrast” and connects them to the case-level ranking and result interpretation.
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