Gene expression profiling in MDA-MB-231 cells following SPRY4-IT1 knockdown. (A) Clusters of genes altered by SPRY4-IT1 knockdown. The heat map reveals clusters of genes. The green color indicates genes that are up regulated compared with the control cells, and the red color indicates genes that down regulated compared with the control cells. The cells in which SPRY4-IT1 was knocked down are presented as A1 and C1, and the control cells are presented as A2, B2 and C2. (B) Top 10 genes significantly upregulated or down regulated in MDA-MB-231 cells following SPRY4-IT1 knockdown. (C, D) The differential gene expression obtained from the microarray analyses was confirmed by qRT-PCR analysis of 10 selected genes using the gene specific primers shown in Additional file 2: Table S1. The data represent the means of triplicate experiments normalized to the GAPDH level and are presented as the relative fold changes (RFC) of the levels in the MDA-MB-231 cells after SPRY4-IT1 knockdown compared with the levels in the Scr-control cells. (E, F) qPCR analysis of the ZNF703 expression levels in MDA-MB-231 and MDA-MB-435S cells after transfection with scrambled siRNA and si-SPRY4-IT1 (E) and in MCF-7 cells after treatment with an empty vector and pcDNA- SPRY4-IT1 (F). The data are presented as the means ± SD from three independent experiments. **P < 0.01. (G) The ZNF703 protein level is elevated in MDA-MB-231 and MDA-MB-435S cells after transfection with si-SPRY4-IT1 and in MCF-7 cells after transfection with pcDNA-SPRY4-IT1.