Supplementary Figure 6: FateID analysis of mouse hematopoietic progenitors. | Nature Methods

Supplementary Figure 6: FateID analysis of mouse hematopoietic progenitors.

From: FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

Supplementary Figure 6

(a, b) The fate bias, corresponding to the probability of a cell to be assigned to a given lineage, is color-coded in the t-SNE map. The fate bias predicted by FateID (left) and STEMNET1 (middle) along with log2-transformed aggregated normalized expression of two lineage markers. Fate bias and marker gene expression is shown for (a) the conventional dendritic cell, and (b) the innate lymphoid lineage. In (a) and (b) data for 1,802 cells from n=4 animals are shown. (c) Scatterplot of normalized expression levels of Kit and Mpo. The predicted neutrophil fate bias is color-coded. Fate bias increases with Mpo expression and is inversely related to the level of Kit. (d) Scatterplot of normalized expression levels of Kit and Tcf4. The predicted pDC fate bias is color-coded. Fate bias increases with Tcf4 expression and is inversely related to the level of Kit. (e) Scatterplot of normalized expression levels of Kit and Ebf1. The predicted B cell fate bias is color-coded. Fate bias increases with Ebf1 expression and is inversely related to the level of Kit. (f) Scatterplot of normalized expression levels of Kit and Car2. The predicted erythrocyte fate bias is color-coded. Fate bias increases with Car2 expression and is inversely related to the level of Kit. (g) Scatterplot of normalized expression levels of Kit and Cd74. The predicted cDC fate bias is color-coded. Fate bias increases with Cd74 expression and is inversely related to the level of Kit. (h) Scatterplot of normalized expression levels of Kit and Tcf7. The predicted NK/NKT/ILC2 fate bias is color-coded. Fate bias increases with Tcf7 expression and is inversely related to the level of Kit. (i-n) Scatterplots comparing fate bias predicted by FateID and STEMNET for (i) the neutrophil, (j) the pDC, (k) the B cell, (l) the erythrocyte, (m) the cDC, and (n) the NK/NKT/ILC lineage. Although the predictions are overall correlated, STEMNET predicts rather uniform levels across a large fraction of the multipotent cell population, suggesting that each cell is multipotent, while FateID predictions sample the full range of possible values for all lineages, comprising cells with zero fate probability, intermediate values, or more substantial bias towards a given lineage. The higher resolution of FateID is potentially explained by the dynamic composition of the training set, which comprises more mature cells during the first iterations, while it includes earlier differentiation stages at later iterations to classify more naïve cells. In contrast to STEMNET, this strategy avoids classifying naïve cells with the help of genes expressed only at late stages of differentiation. In all panels data for 1,802 cells from three independent experiments with n = 4 mice are shown.

1. Velten, L. et al. Human haematopoietic stem cell lineage commitment is a continuous process. Nat. Cell Biol. 19, 271–281 (2017).

Back to article page