Transcription factor binding data
Predicting expression: the complementary power of histone modification and transcription factor binding data
... ChIP-seq data was not normalised to nucleosome density (not assayed), this combination of nucleosome sparsity and TF-modulated chromatin struc- ture presumably explains why HMs provide compara- tively little ...
12
Heat shock protein 70 down-regulates the production of toll-like receptor-induced pro-inflammatory cytokines by a heat shock factor-1/constitutive heat shock element-binding factor-dependent mechanism
... for binding to DNA [53]. The mouse TNF-α promoter contains an HSE binding site for HSF-1 and binding of HSF-1 this HSE results in repressed transcription ...CHBF binding to the HSE on ...
12
Direct, Interferon-Independent Activation of the CXCL10 Promoter by NF-κB and Interferon Regulatory Factor 3 during Hepatitis C Virus Infection
... contains binding sites for several proinflammatory tran- scription factors, we investigated the contribution of these factors to CXCL10 transcriptional induction during HCV infection in ...B binding sites ...
9
Accurate prediction of cell type specific transcription factor binding
... (Additional file 1: Figure S5). Specifically, we consider a bound region conserved if it is also labeled as “bound” in at least three of four training cell types, and we consider a bound region as cell type-specific if ...
17
Identification of transcription factor binding sites using ATAC seq
... HINT is a computational framework for detection of foot- prints from open chromatin data [7]. It works in two major steps: first, genomic cleavage signals are gener- ated from raw sequencing libraries after ...
21
MDM2 promoter SNP285 and SNP309; phylogeny and impact on cancer risk
... In 2004, the group lead by Arnold Levine identified a polymorphism SNP309 (T>G; rs2279744) in the P2 promoter [21]. The G-allele is found across all ethnic groups albeit at a variable frequency (~10% of MDM2 alleles ...
8
The Ensembl Regulatory Build
... public data on epigenetic marks and transcription factor binding in human cell types and used it to construct an intuitive summary of regulatory regions in the human ...more data is ...
8
Why Transcription Factor Binding Sites Are Ten Nucleotides Long
... systematic data on the transcription networks of ...that transcription factors with a larger number of true targets tend to have less total information content (I n) in their binding sites ...
23
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 binding ...
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 ...the binding ...
20
Molecular subtypes of urothelial carcinoma are defined by specific gene regulatory systems
... the transcription factors ELF3, FOXA1 and members of the GATA transcrip- tion factor family [22, 23] (Additional file 2: Figure ...derived transcription factor binding sites obtained ...
15
Identification of an Adeno-Associated Virus Rep Protein Binding Site in the Adenovirus E2a Promoter
... Rep68 binding to the E2a promoter region by ...the binding of purified Rep68 to the 303-bp fragment by ...the binding site in the AAV ...nucleotide binding site) bound to the 303-bp fragment ...
11
The demarcation of transcription factor binding sites through the analysis of DNase seq data
... global transcription-factor-binding patterns that occur following depletion of ...of binding-site ...change transcription-factor assemblies during myeloid differentiation, ...
174
Semen Exosomes Promote Transcriptional Silencing of HIV-1 by Disrupting NF-κB/Sp1/Tat Circuitry
... proviral transcription at multiple transcriptional checkpoints, in- cluding transcription factor recruitment to the long terminal repeat (LTR), tran- scription initiation, and ...human ...
19
Activation of Transcription of the Human Cytomegalovirus Early UL4 Promoter by the Ets Transcription Factor Binding Element
... at the end of this pathway, we determined whether Elk-1 could be one of the cellular proteins bound to the site 2 DNA se- quence. A probe (TNSM6) containing a known Elk-1 site (48) was used in EMSA. Nuclear extracts from ...
13
Temporal Hierarchy of Gene Expression Mediated by Transcription Factor Binding Affinity and Activation Dynamics
... These data suggest that for genes co- regulated by PhoB~P, expression levels are not necessarily corre- lated with affinities of PhoB-binding sites within their ...PhoB~P binding, indicative of low ...
10
Temozolomide analog PMX 465 downregulates MGMT expression in HCT116 colorectal carcinoma cells
... Sp1 binding sites, and transcription factor Sp1 binding could promote MGMT expression(Bocangel et ...Sp1 binding to its consensus site in the MGMT promoter, we performed EMSA using a ...
19
Cell fate control by pioneer transcription factors
... in binding to chromatin is concentration dependent (Gaudet and Mango, ...FOXA binding occurs at genes for various endodermal fates in the endodermal intermediate stage when competence is acquired (Wang et ...
5
Distribution and Dynamics of Transcription-Associated Proteins during Parvovirus Infection
... more-frequent binding to mRNA poly(A) ...partial binding of PABN1-EGFP to immobile speckle ...mRNA binding, and speckle binding times of ...mRNA binding on-rate and adjusted speckle ...
6
The basal transcription machinery as a target for cancer therapy
... Initially, transcription-based therapies were primarily used to inhibit specific oncogenes or key genes required for tumor growth and ...general transcription, highly expressed genes, such as MYC and HIF, ...
15