Fig. 3: Triple-omics integration of the mouse cortex.
From: Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
a–c, UMAP visualizations of the integrated cell embeddings for scRNA-seq (a), snmC-seq (b) and scATAC-seq (c), colored by the original cell types. Cells aligning with ‘mPv’ and ‘mSst’ are highlighted with green circles. Cells aligning with ‘mNdnf’ and ‘mVip’ are highlighted with dark blue circles. Cells aligning with ‘mDL-3’ are highlighted with light blue circles. d, UMAP visualizations of the integrated cell embeddings for all cells, colored by omics layers. e, Significance of marker gene overlap for each cell type across all three omics layers (three-way Fisher’s exact test40). The dashed vertical line indicates that FDR = 0.01. We observed highly significant marker overlap (FDR < 5 × 10−17) for 12 out of the 14 cell types, indicating reliable alignment. For the remaining two cell types, ‘mDL-1’ had marginally significant marker overlap with FDR = 0.003, while the ‘mIn-1’ cells in snmC-seq did not properly align with the scRNA-seq or scATAC-seq cells. f, Coefficient of determination (R2) for predicting gene expression based on each epigenetic layer as well as the combination of all layers (n = 2,677 highly variable genes common to all three omics layers). The box plots indicate the medians (centerlines), means (triangles), first and third quartiles (bounds of boxes) and 1.5× interquartile range (whiskers).
