Fig. 7: Inference of cell type-specific networks for human fetal hematopoiesis data.

a Cell lineage structure linking the cell clusters from scRNA-seq. b Boxplots showing F-scores of n = 11 cell clusters for top 1k edges in predicted networks from scMTNI, scMTNI+Prior, INDEP, INDEP+Prior, and CellOracle compared to gold standard datasets (top). FDR-corrected t-test to compare the F-score of the row algorithm to the F-score of the column algorithm (bottom). The two-sided paired t-test is conducted on F-scores of n = 11 cell clusters for every pair of algorithms. A FDR < 0.05 was considered significantly better. The sign < or > specifies whether the row algorithm’s F-scores were worse or better than the column algorithm’s F-scores. The color scale is specified for − log(FDR), with the red color proportional to significance. Non-significance is colored in gray. In the boxplot, the horizontal middle line of each plot is the median. The bounds of the box are 0.25 quantile (Q₁) and 0.75 quantile (Q₃). The upper whisker is the minimum of the maximum value and Q₃ + 1.5*IQR, where IQR = Q₃ − Q₁. The lower whisker is the maximum of the minimum value and Q₁ − 1.5*IQR. c. Pairwise similarity of networks from each cell cluster using F-score on the top 5k edges. Rows and columns ordered by hierarchical clustering using F-score as the similarity measure. Reconstructed cell lineage trees are shown at the bottom of the pairwise F-score similarity matrix and are constructed using the MST algorithm on the F-score matrix. HSC-MPP hematopoietic stem cells and multipotent progenitors, LMP lymphoid-myeloid progenitors, MEMP MK-erythroid-mast progenitors combined with cycling MEMPs, GP granulocytic progenitors, Ery erythroid cells, Mono monocyte, pDC plasmacytoid dendritic cells. Source data are provided as a Source Data file.