Transcriptional regulation of TCF7L2 and GATA3 target genes. (a) The nearest gene to each TCF7L2 binding site and the nearest gene to each GATA3 binding site was identified and the two lists were compared to identify 3,614 genes that are potentially regulated by both GATA3 and TCF7L2. (b) The expression of the 3,614 GATA3+TCF7L2 bound genes was analyzed in control cells, cells treated with siRNAs to TCF7L2, and cells treated with siRNAs to GATA3; the number of genes whose expression increases or decreases is shown. (c) A scatterplot of expression data from RNA-seq experiments. Each point corresponds to one NCBI Reference Sequence (RefSeq) transcript with fragments per kilobase of gene per million reads (FPKM) values for control and siGATA3 or control and siTCF7L2 knockdown samples shown on a log10 scale. The dashed line represents no change in gene expression between the two samples. Differentially expressed genes whose function corresponds to Gene Ontology categories of breast cancer, cell differentiation, and response to hormone stimulus are highlighted.
Frietze et al. Genome Biology 2012 13:R52 doi:10.1186/gb-2012-13-9-r52