Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors (Q38356146)

2 September 2017

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors (English)

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2 September 2017

2

Martha L Bulyk

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2 September 2017

Michael F Berger

1

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2 September 2017

1 January 2009

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2 September 2017

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2 September 2017

4

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3

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2 September 2017

393-411

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https://scigraph.springernature.com/pub.10.1038/nprot.2008.195

2 September 2017

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cites work

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

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Design of compact, universal DNA microarrays for protein binding microarray experiments

6 September 2017

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Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

6 September 2017

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Specific DNA-binding by apicomplexan AP2 transcription factors

6 September 2017

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Systematic identification of mammalian regulatory motifs' target genes and functions

6 September 2017

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Sequence census methods for functional genomics

6 September 2017

1 reference

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Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure

6 September 2017

1 reference

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Genome-wide mapping of in vivo protein-DNA interactions

6 September 2017

1 reference

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Microarray analyses of newborn mouse ovaries lacking Nobox

6 September 2017

1 reference

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A systems approach to measuring the binding energy landscapes of transcription factors

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Computational identification of transcriptional regulatory elements in DNA sequence

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

DNA microarray technologies for measuring protein-DNA interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Extensive low-affinity transcriptional interactions in the yeast genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Linking DNA-binding proteins to their recognition sequences by using protein microarrays

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Defining the sequence-recognition profile of DNA-binding molecules

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

A global map of p53 transcription-factor binding sites in the human genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Engineering zinc finger protein transcription factors: the therapeutic relevance of switching endogenous gene expression on or off at command

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

enoLOGOS: a versatile web tool for energy normalized sequence logos

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Designing transcription factor architectures for drug discovery.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Parallel, quantitative measurement of protein binding to a 120-element double-stranded DNA array in real time using surface plasmon resonance microscopy

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Quantitative high-throughput analysis of transcription factor binding specificities.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Evaluating the binding affinities of NF-κB p50 homodimer to the wild-type and single-nucleotide mutant Ig-κB sites by the unimolecular dsDNA microarray

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Modulation of DNA-binding domains for sequence-specific DNA recognition

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Additivity in protein-DNA interactions: how good an approximation is it?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Is there a code for protein-DNA recognition? Probab(ilistical)ly. . .

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Exploring the DNA-binding specificities of zinc fingers with DNA microarrays

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Genomic strategies to identify mammalian regulatory sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Chromatin profiling using targeted DNA adenine methyltransferase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Genome-wide location and function of DNA binding proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

DNA binding sites: representation and discovery

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

TRANSFAC: an integrated system for gene expression regulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Quantifying DNA-protein interactions by double-stranded DNA arrays.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

An extradenticle-induced conformational change in a HOX protein overcomes an inhibitory function of the conserved hexapeptide motif

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

The detection of DNA-binding proteins by protein blotting

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Study of protein-DNA interactions by surface plasmon resonance (real time kinetics).

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Inferring condition-specific transcription factor function from DNA binding and gene expression data.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908410

Mouse brain organization revealed through direct genome-scale TF expression analysis

31 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNPROT.2008.195

Structural basis of Hox specificity

31 March 2020

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNPROT.2008.195

MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules

31 March 2020

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNPROT.2008.195

31 March 2020

Identifiers

DOI

10.1038/NPROT.2008.195

1 reference

PMC publication ID

2908410

Dimensions Publication ID

2 September 2017

0 references

1 reference

PMC publication ID

2908410

2 September 2017

PubMed publication ID

19265799

1 reference

PMC publication ID

2908410