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The advent of high throughput sequencing and DNA microarray technologies along with the advances in bioinformatics have revolutionized biological research in the recent years. However, the precise mechanisms that control gene expression are largely unknown despite the numerous efforts to understand them. We describe a bioinformatics technique that can potentially identify condition-specific transcription factor binding sites. We applied our technique to cellular immortalization data set. Our analysis revealed similarities in upstream regions of CXCL gene family that explain condition-specific differential expression of genes CXCL1 and CXCL2, versus gene CXCL3.