(Q34588290)

3 August 2017

title

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome (English)

1 reference

3 August 2017

Chaolin Zhang

1

1 reference

3 August 2017

Zhenyu Xuan

2

1 reference

3 August 2017

Stefanie Otto

3

1 reference

3 August 2017

John R Hover

4

1 reference

3 August 2017

Sean R McCorkle

5

1 reference

3 August 2017

Gail Mandel

6

1 reference

3 August 2017

Michael Q Zhang

7

1 reference

3 August 2017

language of work or name

English

0 references

publication date

2 May 2006

1 reference

3 August 2017

published in

Nucleic Acids Research

1 reference

3 August 2017

volume

34

1 reference

3 August 2017

issue

8

1 reference

3 August 2017

page(s)

2238-2246

1 reference

Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA.

3 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Genome-wide promoter extraction and analysis in human, mouse, and rat.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Genome-scale identification of nucleosome positions in S. cerevisiae

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Alignments anchored on genomic landmarks can aid in the identification of regulatory elements

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

A genetic screen for candidate tumor suppressors identifies REST

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Understanding alternative splicing: towards a cellular code

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

De novo cis-regulatory module elicitation for eukaryotic genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Logic functions of the genomic cis-regulatory code

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Neuron-restrictive silencer factor regulates the N-methyl-D-aspartate receptor 2B subunit gene in basal and ethanol-induced gene expression in fetal cortical neurons.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Discovery of functional noncoding elements by digital analysis of chromatin structure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Transcriptional regulatory code of a eukaryotic genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

How do site-specific DNA-binding proteins find their targets?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

WebLogo: A Sequence Logo Generator

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Statistical analysis of over-represented words in human promoter sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Huntingtin interacts with REST/NRSF to modulate the transcription of NRSE-controlled neuronal genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

MATCH: A tool for searching transcription factor binding sites in DNA sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

TRANSFAC: transcriptional regulation, from patterns to profiles

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Evolution of development in closely related species of flies and worms

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Corepressor-dependent silencing of chromosomal regions encoding neuronal genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Physical constraints and functional characteristics of transcription factor-DNA interaction.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Genome-wide location and function of DNA binding proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

DNA binding sites: representation and discovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Distribution of transcription factor binding sites in the yeast genome suggests abundance of coordinately regulated genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Identification of potential target genes for the neuron-restrictive silencer factor

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

REST: a mammalian silencer protein that restricts sodium channel gene expression to neurons

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

The lac repressor-operator interaction. 3. Kinetic studies

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Lac repressor-operator interaction. I. Equilibrium studies

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Diffusion controlled reaction rates in spheroidal geometry. Application to repressor--operator association and membrane bound enzymes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

On the specificity of DNA-protein interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Facilitated target location in biological systems

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Silencing the type II sodium channel gene: a model for neural-specific gene regulation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

DNAase footprinting a simple method for the detection of protein-DNA binding specificity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Role of NRSF/REST in the molecular mechanisms regulating neural-specific expression of trkC/neurotrophin-3 receptor gene

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Large-scale human promoter mapping using CpG islands.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1456330

Electrophoretic mobility shift assays for the analysis of DNA-protein interactions

27 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16670430

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Kinetic studies on Cro repressor-operator DNA interaction

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16670430

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A cell type-preferred silencer element that controls the neural-specific expression of the SCG10 gene

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16670430

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKL248

1 reference

3 August 2017

1 reference

3 August 2017

1 reference