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Figure 3 | Genome Biology

Figure 3

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 3

Frequency of putative TFBSs in proximal regions of promoters. The promoter sequences were extracted from the over-expressed genes in clusters A and B, and subclusters C1 to C3 in UM-SCC cells using Genomatix Suite 3.4.1. The average length of these promoters was adjusted to approximately 600, including about 500 base pairs upstream and about 100 base pairs downstream from the transcription start site. The promoter sequences from vertebrates represented 159,505 promoters, including 55,207 from human, 69,108 from mouse, and 35,190 from rat in Genomatix promoter database. The P value of transcription factor binding site (TFBS) frequency in a given cluster was calculated by MatInspector of Genomatix Suite 3.4.1. *Significantly increased frequencies of putative binding motifs on promoter regions of clustered genes when compared with the vertebrate promoters with a randomly drawn sample of the same size (P < 0.05). †Significantly lower frequency of the activator protein (AP)-1 binding motif when compared with the vertebrate promoters. EGR, early growth response; NF-κB, nuclear factor-κB; STAT, signal transducer and activator of transcription.

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Genome Biology

ISSN: 1474-760X

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