Fig. 4

Correlations among single cell gene expression, chromatin accessibility, and histone modifications. a Violin plot of correlations among chromatin accessibility and H3K4me2 of transcription factor binding sites for 186 transcription factors. Note that most correlations are strongly positive. b Correlation between chromatin accessibility and H3K4me2 data reveals that targets of pluripotency factors/NuRD complex and targets of Polycomb Group/Trithorax Group proteins are anticorrelated in single cells. c Correlation between gene expression signatures and chromatin accessibility signatures. d Correlation between gene expression signatures and H3K4me2 signatures. e Correlation between gene expression of DNA binding proteins and chromatin accessibility of their targets. f Inferred corresponding values of Sox2 gene expression and chromatin accessibility of SOX2 binding sites. Each point represents inferred correspondence from a single cell. The x-axis shows the value of the gene expression signature in that cell and the y-axis shows the value of the chromatin accessibility signature. The points are colored by inferred master time. g Inferred corresponding values of Yy1 gene expression and chromatin accessibility of YY1 binding sites