Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers (Q37061181)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23554463%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

title

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers (English)

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27 February 2020

1

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27 February 2020

Ewa Szczurek

series ordinal

2

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27 February 2020

Ralf Jauch

series ordinal

3

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27 February 2020

5

Shyam Prabhakar

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27 February 2020

author name string

Jerzy Tiuryn

series ordinal

4

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27 February 2020

publication date

3 April 2013

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27 February 2020

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27 February 2020

volume

23

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27 February 2020

issue

8

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27 February 2020

page(s)

1307-1318

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Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

27 February 2020

cites work

1 reference

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Detection of interacting transcription factors in human tissues using predicted DNA binding affinity

29 September 2017

1 reference

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Deciphering the Sox-Oct partner code by quantitative cooperativity measurements

29 September 2017

1 reference

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Pioneer transcription factors: establishing competence for gene expression

29 September 2017

1 reference

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Animal transcription networks as highly connected, quantitative continua

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Structural basis for the cooperative DNA recognition by Smad4 MH1 dimers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Inferring transcription factor complexes from ChIP-seq data

29 September 2017

1 reference

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Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

29 September 2017

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A user's guide to the encyclopedia of DNA elements (ENCODE)

29 September 2017

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Finding subtypes of transcription factor motif pairs with distinct regulatory roles

29 September 2017

1 reference

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Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Nucleosome-mediated cooperativity between transcription factors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Evolution of the repertoire of nuclear receptor binding sites in genomes

29 September 2017

1 reference

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Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

An atlas of combinatorial transcriptional regulation in mouse and man

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

DNA specificity determinants associate with distinct transcription factor functions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Detection of nonneutral substitution rates on mammalian phylogenies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

F-Seq: a feature density estimator for high-throughput sequence tags

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Integration of external signaling pathways with the core transcriptional network in embryonic stem cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Quantifying similarity between motifs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Direct interactions of Runx2 and canonical Wnt signaling induce FGF18.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1

29 September 2017

1 reference

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Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation.

29 September 2017

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Coot: model-building tools for molecular graphics

29 September 2017

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Structural basis of androgen receptor binding to selective androgen response elements.

29 September 2017

1 reference

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Transcription regulation and animal diversity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Lymphoid enhancer factor-1 and beta-catenin inhibit Runx2-dependent transcriptional activation of the osteocalcin promoter

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Hepatocyte nuclear factor 1 alpha controls renal expression of the Npt1-Npt4 anionic transporter locus

29 September 2017

1 reference

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Predicting transcription factor synergism

29 September 2017

1 reference

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

29 September 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Synergistic activation of the fibroblast growth factor 4 enhancer by Sox2 and Oct-3 depends on protein-protein interactions facilitated by a specific spatial arrangement of factor binding sites

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

TRANSFAC: a database on transcription factors and their DNA binding sites

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

The p53 protein is an unusually shaped tetramer that binds directly to DNA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Recognition DNA sequences of interferon regulatory factor 1 (IRF-1) and IRF-2, regulators of cell growth and the interferon system

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Purified hepatocyte nuclear factor 1 interacts with a family of hepatocyte-specific promoters

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Direct repeats as selective response elements for the thyroid hormone, retinoic acid, and vitamin D3 receptors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

How p53 binds DNA as a tetramer

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

On the power of profiles for transcription factor binding site detection.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3730104

4 September 2018

Identifiers

DOI

10.1101/GR.154922.113

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27 February 2020

1 reference

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27 February 2020

1 reference

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