Comparative analysis of genome-wide GABPα occupancy and expression profiles by GSEA broadens GABP direct target genes/pathways. (A) GSEA profile of correlation between GABP-regulated genes and GABP-bound gene set. GABP-activated direct targets are at the leading edge of positive correlation (in red box on the left), and GABP-repressed direct targets are at the leading edge of negative correlation (in blue box on the right). Functional annotation of these 2 subsets is summarized in supplemental Table 3. (B) Downstream transcription factors that are regulated by both GABP and Scl/Tal1. Shown is the heatmap with color-coded scale bars showing Z-scores. (C) GSEA profiles of correlation between genes positively regulated by GABP and gene sets containing stem cell signatures. (D) GSEA profile of correlation between genes negatively regulated by GABP and a gene set containing genes enriched in mature blood cells compared with HSCs (shared between fetal liver and adult BM HSCs). Other negatively correlated gene sets include HSC_MATURE_FETAL (P = 0, false discovery rate [FDR] q = 0.009) and HSC_MATURE_ADULT (P = 0, FDR q = 0.069) in GSEA, containing genes up-regulated in mature blood cells compared with fetal liver and BM HSCs, respectively (both from Ivanova et al³⁸ ). (E) GSEA profiles of correlation between genes positively regulated by GABP and gene sets of select pathways. For all the GSEA in panels A and C-E, enrichment plots are shown, with gene set names, nominal P values, and FDR q values marked on top of the plots. More detailed description of all the gene sets in panels C through E, genes at the leading edge, and heatmaps are given in supplemental Figure 3. Note that a reported P = 0 indicates an actual P < 1/number of permutations. In our analysis the number of permutations was set at 1000, and thus the reported “P = 0” is equivalent to P < .001.