Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences (Q36865636)

16 August 2017

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

1 reference

16 August 2017

9

Olga B Botvinnik

1 reference

16 August 2017

Esther T Chan

10

0 references

Quaid D Morris

object named as

Quaid D Morris

15

0 references

Martha L Bulyk

16

object named as

Martha L Bulyk

1 reference

16 August 2017

Michael F Berger

1

1 reference

16 August 2017

Gwenael Badis

2

1 reference

16 August 2017

Andrew R Gehrke

3

1 reference

16 August 2017

Shaheynoor Talukder

4

1 reference

16 August 2017

Anthony A Philippakis

5

1 reference

16 August 2017

Lourdes Peña-Castillo

6

1 reference

16 August 2017

Trevis M Alleyne

7

1 reference

16 August 2017

Sanie Mnaimneh

8

1 reference

16 August 2017

Faiqua Khalid

11

1 reference

16 August 2017

Wen Zhang

12

1 reference

16 August 2017

Daniel Newburger

13

1 reference

16 August 2017

Savina A Jaeger

14

1 reference

16 August 2017

Timothy R Hughes

17

1 reference

16 August 2017

language of work or name

English

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publication date

1 June 2008

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16 August 2017

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16 August 2017

133

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16 August 2017

7

1 reference

16 August 2017

1266-1276

1 reference

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

A murine specific expansion of the Rhox cluster involved in embryonic stem cell biology is under natural selection

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Core transcriptional regulatory circuitry in human hepatocytes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Hox transcription factors and their elusive mammalian gene targets

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Transcriptional regulatory code of a eukaryotic 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=2531161

Role of intrinsic DNA binding specificity in defining target genes of the mammalian transcription factor PDX1

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

The Mouse Genome Database (MGD): integrating biology with the 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=2531161

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

TRANSFAC: transcriptional regulation, from patterns to profiles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

The Homeodomain Resource: 2003 update

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Hox repression of a target gene: extradenticle-independent, additive action through multiple monomer 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=2531161

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Obox, a family of homeobox genes preferentially expressed in germ 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=2531161

Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

A comparison of in vivo and in vitro DNA-binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

A molecular code dictates sequence-specific DNA recognition by homeodomains.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Extra specificity from extradenticle: the partnership between HOX and PBX/EXD homeodomain 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=2531161

29 September 2017

Homeodomain interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Binding of myc proteins to canonical and noncanonical DNA sequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

The DNA-binding specificity of the hepatocyte nuclear factor 3/forkhead domain is influenced by amino-acid residues adjacent to the recognition helix

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Functional specificity of the Antennapedia homeodomain

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

The segment identity functions of Ultrabithorax are contained within its homeo domain and carboxy-terminal sequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Nucleotides flanking a conserved TAAT core dictate the DNA binding specificity of three murine homeodomain 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=2531161

Multiple Otx binding sites required for expression of the Strongylocentrotus purpuratus Spec2a gene

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

The degree of variation in DNA sequence recognition among four Drosophila homeotic 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=2531161

Identification of novel DNA binding targets and regulatory domains of a murine tinman homeodomain factor, nkx-2.5.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

A single amino acid can determine the DNA binding specificity of homeodomain 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=2531161

DNA specificity of the bicoid activator protein is determined by homeodomain recognition helix residue 9

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

DNA binding specificity of homeodomains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Differential DNA sequence recognition is a determinant of specificity in homeotic gene action.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Mapping functional specificity in the Dfd and Ubx homeo domains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

The NK homeobox gene cluster predates the origin of Hox genes

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Hand is a direct target of Tinman and GATA factors during Drosophila cardiogenesis and hematopoiesis

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531161

Structural basis of Hox specificity

4 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18585359

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18585359

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.CELL.2008.05.024

1 reference

16 August 2017

1 reference

16 August 2017

PubMed publication ID

18585359

1 reference