Transcription factor binding sites
Transcription factor binding sites are highly enriched within microRNA precursor sequences
... more transcription factor binding sites, as defined by the same algorithms and stringent statisti- cal criteria that are used for TFBS within ...that transcription factors bind pri- ...
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Mapping genome-wide transcription factor binding sites in frozen tissues
... of binding sites for Rnap2, Ctcf, and Rxrα in mouse liver (Figure 2A and Additional file 1: Table ...that binding sites were enriched for their known canonical binding motifs (Figure ...
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The demarcation of transcription factor binding sites through the analysis of DNase seq data
... However, the types of assays performed by the ENCODE project that charac- terise the location, and in some cases, the transcription factor binding sites, do not identify where in the genome an ...
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DNA Replication Efficiency Depends on Transcription Factor-Binding Sites
... Sp1 transcription factor-binding sites in pairs, while AP-1 sites are found ...Sp1 sites and an AP-1 site and the other with two pairs of Sp1 sites and two single AP-1 ...
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PhyloScan: identification of transcription factor binding sites using cross-species evidence
... predicted transcription factor binding sites) fall into two general ...of transcription factor binding sites and a scoring scheme to evaluate predictions ...
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Why Transcription Factor Binding Sites Are Ten Nucleotides Long
... of binding-site lengths and specificities found in both prokaryotes and ...prokaryotic binding sites tend to be longer on average (Figure ...cooperative binding in eukaryotes, which tend to ...
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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 ...
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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 ...the ...
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Number of active transcription factor binding sites is essential for the Hes7 oscillator
... Her7 transcription by Her7 is repre- sented by an inhibitory Hill ...between transcription factor binding ...single binding site for Hes7 ...By transcription analysis they ...
6
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 ...the ...
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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
Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites
... TF/uDBP binding sites offers a valuable approach, and we have shown that this can facilitate discovery of cis-regulatory modules, design of targeted dODN therapies, and interpretation of GWAS hits at ...
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Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites
... and binding site representation Plants are constantly surrounded by stimulus, be-they deletorious pathogens or positive stimuli such as light and ...as transcription factors (TFs) to facilitate ...
11
Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites
... DNAm patterns were measured in two fibroblast prepa- rations at early (P3 or P5) and late passages (P30 or P33). To this end, we used MethylCap-seq, which is based on capturing methylated DNA with the methyl- ...
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Characterization of functional Sp1 transcription factor binding sites in the hepatitis B virus nucleocapsid promoter.
... To investigate further the possibility that the same or similar factors might be binding to the nucleocapsid CpA, CpB, and CpC and major surface antigen B, D, D5', E, F, and F3' promoter[r] ...
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Locus-specific hypomethylation of the mouse IAP retrotransposon is associated with transcription factor-binding sites
... Although most of the genomic IAP LTR copies were heavily methylated in the sperm and tail, we found that LTRs of a specific subfamily exhibited a tendency to be hypomethylated, especially when specific sequences were ...
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Identification of transcription factor binding sites using ATAC seq
... Fig. 2 Strategies for cleavage bias correction. Comparison of bias estimation methods in standard ATAC-seq (a) and DNase-seq (b) on 32 TF ChIP-seq data sets from GM12878 cells. The y-axis denotes the ranking score, where ...
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Multiple transcription factor binding sites mediate adenovirus E1A transactivation.
... To avoid the complications inherent in studying early adenovirus promoters which contain binding sites for multiple transcription factors implicated in ElA transactivation, we synthesize[r] ...
8
Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates
... in transcription factor binding sites in the promot- ers and, therefore, potential differential gene regulation, we dissected the proximal promoter regions of both ...putative binding ...
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Computational Methods for Identifying and Characterizing the Human Gene Regulatory Regions and Cis-elements
... notably transcription factor binding sites (TFBS) in the anking non-coding regions of ...The binding of transcription factors to specic cis-regulatory elements, typically those ...
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