Factor Binding-Sites
TBXA2R rSNPs, Transcriptional Factor Binding Sites and Asthma in Asians
... Four linked TBXA2R single nucleotide polymorphisms (SNPs, rs2238631, rs2238632, rs2238633 and rs2238634) which span a 431bp region of intron one have been found to be in linkage disequilibrium (LD) with two exon 3 SNPs ...
14
Most transcription factor binding sites are in a few mosaic classes of the human genome
... Figure 1 The mosaic classes of the human genome. Each circle represents one of the mosaic classes. The position of the circle shows the A/C/G/ T content:-(a) T+C by A+T, (b) T+G by A+T, (c) T+G by T+C. The area of the ...
18
The design of transcription factor binding sites is affected by combinatorial regulation
... transcription factor binding sites ...which binding sites are short and fuzzy, precisely because spurious appearances will occur relatively frequently ...each factor ensures that ...
10
ATF3 rSNPs, transcriptional factor binding sites and human etiology
... transcription factor 3 (ATF3) gene is a member of the activating transcription factor/cAMP re- sponsive element binding (CREB) protein family of transcription factors, which share the basic ...
9
Analysis of variation at transcription factor binding sites in Drosophila and humans
... ’ binding sites and could therefore be used to compare such constraints across TFBS instances, as presented ...of sites showing variation) and specificity of the analysis, resulting in the final ...
15
Identification of transcription factor binding sites using ATAC seq
... We evaluate here the use of position dependency models (PDM) to estimate the bias of Tn5 cleavage events. HINT- ATAC considers the fifth base of ATAC-seq reads as the cleavage event as in [5]. A PDM learns relevant ...
21
Functional analysis of transcription factor binding sites in human promoters
... transcription factor complex, which recognizes IFN-stimulated response element (ISRE) DNA sequences (AGTTTNNNTTTCC) ...on binding sites for (STAT1:STAT1) homodimers recognizing GAS ...
16
AKT3 rSNPs, Transcriptional Factor Binding Sites and Human Disease
... transcriptional factor (TF) will usually recognize a number of different binding sites in the ...TF binding which results in allele-specific gene ...natural binding site or generate a ...
14
Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome
... transcription factor binding sites TRANSFAC database (release ...(confirmed sites); the TFBS sequence can be found within 5 kb upstream of the TSS; if multiple site occurrences are present in ...
18
A computational approach for genome wide mapping of splicing factor binding sites
... splicing factor binding sites (SFBSs) have been developed ...experimental binding data (for example, [26]); for a review, see ...core binding motif and do not consider genomic ...
14
Co regulation by Notch and Fos is required for cell fate specification of intermediate precursors during C elegans uterine development
... cis binding elements are required for egl-13 expression at cell specification and for rescue of egl-13 mutant ...transcription factor binding sites within the ...Trans factor ...
11
Genome wide prediction of transcription factor binding sites using an integrated model
... binding sites only represented a portion of enhancers and the training histone data might not fully capture the chro- matin signature associated with TFBSs in ...the binding sites of these TFs ...
17
Variable structure motifs for transcription factor binding sites
... DNA-transcription factor binding sites (TFBSs) have been based on relatively few known instances and have treated them as sites of fixed length using position weight matrices ...transcription ...
19
Variable structure motifs for transcription factor binding sites
... DNA-transcription factor binding sites (TFBSs) have been based on relatively few known instances and have treated them as sites of fixed length using position weight matrices ...transcription ...
20
The demarcation of transcription factor binding sites through the analysis of DNase seq data
... All of the aforementioned analyses rely on ChIP-seq data as a gold standard, and therefore false positives in ChIP-seq analyses can appear as false negatives in foot- printing assays and vice versa. Other metrics that do ...
174
Replication from oriP of Epstein-Barr Virus Requires Exact Spacing of Two Bound Dimers of EBNA1 Which Bend DNA
... between sites 2 and 3 but 7 bp closer to site 2. This put sites 1 and 2 closer to the center of the DNA fragment than sites 3 and 4, so the net bend caused by EBNA1 binding at sites 1 ...
9
Effect of positional dependence and alignment strategy on modeling transcription factor binding sites
... the probability that the known negative example would score higher than the known positive example — produc- ing a false positive. PS scopes larger than a certain value do not capture any new position-pair matches, yet ...
11
Patients with Congenital Factor V Deficiency have Decreased Factor Xa Binding Sites on their Platelets
... of Factor X a from Factor V-deficient patients was normal when platelet binding was ...contains Factor V activity, corrected the Factor X a binding deficiency of the platelets ...
9
Regulation of bovine beta defensin expression
... the binding of transcription factors to both gene-proximal and distal non-coding DNA in a context-specific manner, understanding of how this process controls the expression of β-defensin genes could help identify ...
283
Protein ligand interactions: docking, design and protein conformational change
... OmpA is a highly conserved outer membrane protein of E. coli with a molecular weight of ~35 kDa (325 amino acids) containing eight transmembrane domains and four extracellular loops. The crystal structure of the ...
353