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Transcription factor-DNA binding: beyond binding site motifs.
scientific article published on 27 March 2017
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14 March 2020
title
Transcription factor-DNA binding: beyond binding site motifs
(English)
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14 March 2020
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Sachi Inukai
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14 March 2020
Martha L Bulyk
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Martha L Bulyk
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Kian Hong Kock
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publication date
27 March 2017
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14 March 2020
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Current Opinion in Genetics & Development
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14 March 2020
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43
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14 March 2020
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14 March 2020
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Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
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stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
MEME-ChIP: motif analysis of large DNA datasets
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Determining the specificity of protein-DNA interactions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Deep and wide digging for binding motifs in ChIP-Seq data.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Origins of specificity in protein-DNA recognition.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Variation in transcription factor binding among humans
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Hox specificity unique roles for cofactors and collaborators
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
MEME SUITE: tools for motif discovery and searching
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Diversity and complexity in DNA recognition by transcription factors
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
A census of human transcription factors: function, expression and evolution
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
A systems approach to measuring the binding energy landscapes of transcription factors
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
DNA binding sites: representation and discovery
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Sequence logos: a new way to display consensus sequences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
17 June 2018
Competition between DNA methylation and transcription factors determines binding of NRF1.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
21 August 2018
Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
21 August 2018
A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
21 August 2018
High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5447501
retrieved
21 August 2018
Population Variation and Genetic Control of Modular Chromatin Architecture in Humans
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/28359978
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1016/J.GDE.2017.02.007
1 reference
stated in
Europe PubMed Central
PMCID
5447501
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28359978%20AND%20SRC:MED&resulttype=core&format=json
retrieved
14 March 2020
Fatcat ID
release_b3h57qji4vch5beb3u27cu5qky
1 reference
stated in
Fatcat
reference URL
https://api.fatcat.wiki/v0/release/b3h57qji4vch5beb3u27cu5qky
retrieved
24 November 2022
based on heuristic
mapped directly with Wikidata item
PMCID
5447501
1 reference
stated in
Europe PubMed Central
PMCID
5447501
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28359978%20AND%20SRC:MED&resulttype=core&format=json
retrieved
14 March 2020
PubMed ID
28359978
1 reference
stated in
Europe PubMed Central
PMCID
5447501
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28359978%20AND%20SRC:MED&resulttype=core&format=json
retrieved
14 March 2020
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