MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures
Fig 5
+ compartments by MaxComp and its comparison with other methods on mESC Chr5 and Chr15 (A) The experimental profile obtained from the Hi-C-based principal component analysis and the compartment profile predicted by MaxComp on 886 SeqFISH+ structures [8] of mESC Chr5. (B) The experimental profile obtained from the Hi-C-based principal component analysis and the compartment profile predicted by MaxComp on 884 SeqFISH+ structures of mESC Chr15. (C) Scatter plot between the normalized compartment frequencies of MaxComp and the PC1 values together with the Pearson’s correlation coefficient between the two samples on each chromosome. (D) Scatter plot of compartment variabilities against PC1 values from the Hi-C-based PCA annotations on each chromosome. Each dot represents a genomic region colored by its value of speckle distance variability. (E) Comparison of compartmentalization scores between the Hi-C-based PCA annotation, the MaxComp prediction, the distance-based PCA annotation and the CG phasing prediction for each structure on mESC Chr5 and Chr15 showed together with the corresponding violin plots. (F) The 3D visualization of 6 selected SeqFISH+ structures of mESC Chr5 colored by compartments (red in compartment A and blue in compartment B) from both experiment and the MaxComp prediction. (G) Log fold change of the average transcription level (number of mRNA transcript spots detected) of cells with both copies labeled with A (A cells) against the level of cells with both copies labeled with B (B cells) for each gene.