Supplementary Figure 9: Trans regulators of hematopoiesis.

(a) Summary of motif usage across hematopoiesis. The values shown represent normalized relative deviation scores. Relative deviation scores for representative transcription factor motifs are shown in Figure 4b,c. Scores are normalized by the maximum and minimum (range) across the 13 cell types assayed, such that the values shown range from 0 to 1. The range for the raw scores is shown above each column. Raw values can be found in Supplementary Table 3. (b) Unsupervised hierarchical clustering of hematopoiesis transcription factor motifs (n = 46; rows) with in vitro–derived motifs (CIS-BP) (n = 806; columns). Values shown represent motif similarity using Pearson correlation (Online Methods). Boxes highlight clustered CIS-BP motifs. (c,d) Examples of individual motif PWMs from clustered motifs as in b for the GATA (c) and MEIS1 (d) hematopoiesis transcription factor motifs. The top row represents a hematopoietic TF motif and subsequent rows show similar CIS-BP motifs from the cluster analysis. (e) Histogram of all correlation values in b. A correlation cutoff of 0.8 was used to assign potential regulators to motifs. Putative hematopoietic regulators are highlighted (n = 255). (f) Correlation of motif deviation scores to gene expression changes across hematopoietic cell types for two developmentally important transcription factors, GATA1 and PAX5. Each point represents a cell type comparison (for example, HSC versus MPP). Error bars, error in the gene expression measurement, as estimated by DESeq2. (g,h) Summary list of putative transcription factor positive (g) and negative (h) regulators of hematopoiesis motifs. Motifs are listed on the left, and the names of the genes predicted to regulate that motif are listed on the right. Values represent correlation coefficients (Pearson) comparing changes in motif deviation scores to the expression of putative regulators, as shown in f and Figure 4e, only the most correlated gene is shown here; a full list of correlation coefficients and P values can be found in Supplementary Table 4.