Strong association between genomic 3D structure and CRISPR cleavage efficiency
Fig 5
3D features improve prediction in non-matching cell types.
(A) Correlations between 3D features, generated from Hi-C in T/HEK293/GM12878 cells, and CRISPR efficiency. (B-C) Blue/orange/green bars represent 3D features generated from Hi-C in T/HEK293/GM12878 cells, respectively. (B) Relative change in xgboost r2 before and after adding a 3D feature to the model. (C) Rank of the 3D features relative to the other features, based on their average SHAP rank in the 1000 xgboost iterations; a higher rank is better. The dashed line represents the theoretical rank of a feature ranked first in all 1000 models.