TLX1 and NOTCH coregulate transcription. (A) ALL-SIL cells were treated for 24 hours with 500 nM Compound E (GSI) and 0.05% DMSO as vehicle control and then harvested for microarray analysis. The Venn diagrams indicate a significant overlap between TLX1 targets and GSI-responsive genes (P < 0.0001; data for a 10% FDR is shown). GO terms uniquely associated with the overlapping genes in each pair-wise comparison are indicated (see text for details). (B) Hierarchical clustering of known genes showing > 2-fold change under TLX1High versus TLX1Low conditions and a FDR < 10%. (C) Confirmation by qRT-PCR of representative coregulated genes. Data is normalized to TLX1Low GSI-treated samples, where both NOTCH and TLX1 are downregulated. The average of 3 experiments is shown (P values are indicated in the text where discussed and the P values for all comparisons are provided in Additional file 4; n = 3 biological replicates, each comprising 3 technical replicates). (D) TLX1 and NOTCH repress the GAS1 gene via a TLE corepressor-mediated mechanism. Top, ALL-SIL cells expressing the TX1 shRNA95 or pLKO control vector were transduced with lentiviral vectors expressing panTLE shRNAs. Bottom, ALL-SIL cells expressing the pLKO control vector were transduced with lentiviral vectors expressing panTLE shRNAs. GSI treatment was for 24 hours. (E) Western blot analysis showing 50% reduced TLE1 levels in ALL-SIL cells expressing panTLE shRNAs (P < 0.05).