Ikaros target genes are differentially expressed in the context of hematopoiesis, lymphocyte lineage choice, and B-cell differentiation. (A) Ikaros target genes are differentially expressed during B-cell lineage specification in vivo. Vertical arrows describe gene expression changes at the respective developmental transitions (up for up-regulation, down for down-regulation). Left: arrow color indicates if Ikaros-regulated genes are enriched among up- and down-regulated genes in vivo (see color scale). Right: arrow color indicates if Ikaros-bound genes are enriched among up- and down-regulated genes in vivo. Supplemental Excel File 4 lists the genes that are regulated by Ikaros in B3 cells and differentially expressed during B-cell lineage specification. (B) Ikaros target genes are differentially expressed during the transition from proliferating to resting pre-B cells in vivo. Arrows describe gene expression changes at the developmental transition from the cycling to resting pre-B cells (up for up-regulation, down for down-regulation). Left: arrow color indicates if Ikaros-regulated genes are enriched among up- and down-regulated genes in vivo (see color scale). Right: arrow color indicates if Ikaros-bound genes are enriched among up- and down-regulated genes in vivo. Supplemental Excel File 4 lists the genes that are regulated by Ikaros in B3 cells and differentially expressed during the progression from Fr.C' to Fr.D. (C) Ikaros expression in B3 cells captures most gene expression changes that occur during the transition from proliferating to resting pre-B cells in vivo. The Venn diagram on the right shows down-regulated genes. (D) Heat map of mean-centered T-statistics for Pearson correlations between B3 cells and successive stages of B-cell progenitor differentiation. Control B3 cells most resemble Fr. C’ proliferating pre-B cells and Ikaros-transduced B3 cells most resemble Fr. D resting pre-B cells. (E) Heat map of developmental stage-specific gene expression changes during B-cell differentiation in vivo (relative to the population average) and gene expression changes induced by Ikaros expression in B3 cells. A hierarchical tree based on Spearman's rank correlation shows pairwise distances between populations. (F) Primary pre-B cells expanded on ST2 feeder cells in the presence of interleukin-7 were transduced with Ikaros-IRES-GFP or IRES-GFP control vector as described¹³  and sorted for GFP expression 48 h later. Gene expression changes were determined using Affymetrix arrays for 2 biological replicates and results were overlaid with developmental gene expression data as described in A and B. Supplemental Excel File 5 lists the genes that are regulated by Ikaros in primary pre-B cells and differentially expressed during B-cell lineage specification and the progression from Fr.C' to Fr.D.