Interrogation of binding site motifs associated with genes regulated by stable LMO2 transfection. (A) Differentially expressed genes were evaluated for enrichment of specific binding site motifs in their promoter region by comparison to the C3 motif gene sets that are part of mSigDB, using Nextbio, as described in supplemental Methods. The occurrence of a motif for specific binding factor in the promoter of a particular gene is indicated by a black square. The mean log₂ expression change of each gene between control and LMO2-transfected experiments is shown (red indicates up-regulation by LMO2 transfection). Genes that did not have a binding motif for the factors found to be significant are not shown. (B) All genes were ranked by their mean change in expression between control and LMO2-transfected lines. Gene set enrichment analysis was used to evaluate the distribution of genes with predicted SP1 and LEF1 binding sites in their promoter regions. In both cases, SP1 and LEF1 target genes were generally down-regulated by LMO2 transfection (both P < .001 by Kolmogorov-Smirnov test).