Journal: Genome Biology

Article Title: 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

doi: 10.1186/gb-2007-8-5-r78

Figure Lengend Snippet: 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.

Article Snippet: To determine the potential conservation of the predicted TFBSs, the orthologous promoter regions of genes in clusters A and B were examined by searching their conservation at the sequence level among vertebrates (human, mouse, and rat) using the comparative genomics analysis feature of Genomatix Suite 3.4.1.

Techniques: Binding Assay

Journal: Genome Biology

Article Title: 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

doi: 10.1186/gb-2007-8-5-r78

Figure Lengend Snippet: 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.

Article Snippet: To determine the potential conservation of the predicted TFBSs, the orthologous promoter regions of genes in clusters A and B were examined by searching their conservation at the sequence level among vertebrates (human, mouse, and rat) using the comparative genomics analysis feature of Genomatix Suite 3.4.1.

Techniques: Binding Assay, Sequencing

Journal: Genome Biology

Article Title: 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

doi: 10.1186/gb-2007-8-5-r78

Figure Lengend Snippet: Transcription regulatory module containing multiple transcription factors in eight histone gene promoters from cluster A. Using FrameWorker of Genomatix Suite 3.4.1, eight promoter regions of histone genes (two H2A and six H2B) from cluster A were used to predict regulatory modules including TBPF (TATA-binding protein factors), ECAT (enhancer of CCAAT binding factors), or PCAT (promoter of CCAAT binding factors). p53 binding motifs were also displayed. '(+)' and '(-)' refer to strand direction of transcription factor binding motifs.

Article Snippet: To determine the potential conservation of the predicted TFBSs, the orthologous promoter regions of genes in clusters A and B were examined by searching their conservation at the sequence level among vertebrates (human, mouse, and rat) using the comparative genomics analysis feature of Genomatix Suite 3.4.1.

Techniques: Binding Assay