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Figure 4 | Genome Biology

Figure 4

From: Genome-wide identification of novel expression signatures reveal distinct patterns and prevalence of binding motifs for p53, nuclear factor-κB and other signal transcription factors in head and neck squamous cell carcinoma

Figure 4

Predicted conserved p53 and NF-κB binding sites in proximal promoter regions of five representative genes from clusters A and B. The search for conserved TFBS was carried out by multiple sequence alignment of each promoter set using DiAlignTF of Genomatix Suite 3.4.1. The promoter region included about 500 base pairs upstream and about 100 base pairs downstream from the transcription start site (TSS) among human, chimpanzee, mouse, and rat. (a) The conserved p53 binding motifs were present in two gene promoters from cluster A (CPS1 and ARID1A), and (b) conserved nuclear factor-κB (NF-κB) binding motifs were present in three gene promoters from cluster B (ICAM1, IL6, and CA9). Letters in bold are the predicted binding sites of p53 or NF-κB, letters in italic are early growth response (EGR)1 binding sites, and letters underlined denote the core conserved sequence. The numbers showed predicted transcription factor binding site (TFBS) position from the TSS of human sequences, where negative positions were upstream of the TSS and positive ones were downstream from the TSS.

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