Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm (Q21563555)

Caudal Dmel_CG1759

1 reference

Even skipped Dmel_CG2328

1 reference

Bicoid Dmel_CG1034

1 reference

Knirps Dmel_CG4717

1 reference

Giant Dmel_CG7952

1 reference

Hunchback Dmel_CG9786

1 reference

21

Michael B Eisen

Michael B

Eisen

1 reference

22 September 2022

Richard Bourgon

3

Richard

Bourgon

1 reference

22 September 2022

20

Terence P Speed

Terence P

Speed

1 reference

22 September 2022

17

Susan E Celniker

Susan E

Celniker

1 reference

22 September 2022

Xiao-yong Li

1

Xiao-yong

Li

1 reference

22 September 2022

Stewart MacArthur

2

Stewart

MacArthur

1 reference

22 September 2022

David Nix

4

David

Nix

1 reference

22 September 2022

Daniel A Pollard

5

Daniel A

Pollard

1 reference

22 September 2022

Venky N Iyer

6

Venky N

Iyer

1 reference

22 September 2022

Aaron Hechmer

7

Aaron

Hechmer

1 reference

22 September 2022

Lisa Simirenko

8

Lisa

Simirenko

1 reference

22 September 2022

Mark Stapleton

9

Mark

Stapleton

1 reference

22 September 2022

Cris L Luengo Hendriks

10

Cris L

Luengo Hendriks

1 reference

22 September 2022

Hou Cheng Chu

11

Hou Cheng

Chu

1 reference

22 September 2022

Nobuo Ogawa

12

Nobuo

Ogawa

1 reference

22 September 2022

William Inwood

13

William

Inwood

1 reference

22 September 2022

Victor Sementchenko

14

Victor

Sementchenko

1 reference

22 September 2022

Amy Beaton

15

Amy

Beaton

1 reference

22 September 2022

Richard Weiszmann

16

Richard

Weiszmann

1 reference

22 September 2022

David W Knowles

18

David W

Knowles

1 reference

22 September 2022

Tom Gingeras

19

Tom

Gingeras

1 reference

22 September 2022

Mark D Biggin

22

Mark D

Creative Commons Attribution 4.0 International

Biggin

1 reference

22 September 2022

language of work or name

English

0 references

publication date

February 2008

0 references

published in

PLOS Biology

0 references

volume

6

0 references

issue

2

0 references

page(s)

e27

0 references

copyright license

start time

12 February 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

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Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

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Transcriptional control in the segmentation gene network of Drosophila

19 March 2017

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Position specific variation in the rate of evolution in transcription factor binding sites

19 March 2017

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Systematic determination of patterns of gene expression during Drosophila embryogenesis

19 March 2017

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

19 March 2017

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19 March 2017

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19 March 2017

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Regulation of even-skipped stripe 2 in the Drosophila embryo

19 March 2017

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19 March 2017

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

19 March 2017

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Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex

19 March 2017

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WebLogo: A Sequence Logo Generator

19 March 2017

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Exploration, normalization, and summaries of high density oligonucleotide array probe level data

19 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

19 March 2017

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The genome sequence of Drosophila melanogaster

19 March 2017

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Fitting a mixture model by expectation maximization to discover motifs in biopolymers

19 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Genome-wide location and function of DNA binding proteins

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

DNA binding sites: representation and discovery

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Mutations affecting segment number and polarity in Drosophila

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Two gap genes mediate maternal terminal pattern information in Drosophila

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Genome-wide mapping of in vivo protein-DNA interactions

19 March 2017

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

7 April 2017

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A gene complex controlling segmentation in Drosophila

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Phosphorylation and functions of the RNA polymerase II CTD

7 April 2017

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

7 April 2017

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Transcription regulation and animal diversity

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences

7 April 2017

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Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome

7 April 2017

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Global analysis of patterns of gene expression during Drosophila embryogenesis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

A core transcriptional network for early mesoderm development in Drosophila melanogaster

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Model-based analysis of tiling-arrays for ChIP-chip.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Spatial regulation of microRNA gene expression in the Drosophila embryo.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

TileMap: create chromosomal map of tiling array hybridizations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Combining phylogenetic and hidden Markov models in biosequence analysis

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Recruitment of the proneural gene scute to the Drosophila sex-determination pathway.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Dorsal gradient networks in the Drosophila embryo

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Transcriptional regulation in Drosophila: the post-genome challenge

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Transcriptional repression: the long and the short of it.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Accessibility of transcriptionally inactive genes is specifically reduced at homeoprotein-DNA binding sites in Drosophila

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

An in vivo UV crosslinking assay that detects DNA binding by sequence-specific transcription factors

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Evidence for stabilizing selection in a eukaryotic enhancer element.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

The specificity of protein-DNA crosslinking by formaldehyde: in vitro and in drosophila embryos

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Zeste-mediated activation by an enhancer is independent of cooperative DNA binding in vivo

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Regulation of two pair-rule stripes by a single enhancer in the Drosophila embryo

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

DNA binding specificity of two homeodomain proteins in vitro and in Drosophila embryos.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

The eve stripe 2 enhancer employs multiple modes of transcriptional synergy

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Non-specific DNA binding of genome regulating proteins as a biological control mechanism: I. The lac operon: equilibrium aspects

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Protein database searches for multiple alignments

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

The origin of pattern and polarity in the Drosophila embryo

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Transcription factor access to chromatin

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Molecular mechanisms of cell-type determination in budding yeast

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Comparison of protein binding to DNA in vivo and in vitro: defining an effective intracellular target.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

From gradients to stripes in Drosophila embryogenesis: filling in the gaps

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Two homeo domain proteins bind with similar specificity to a wide range of DNA sites in Drosophila embryos.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Ultraviolet cross-linking assay to measure sequence-specific DNA binding in vivo.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

The enhanceosome and transcriptional synergy.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Regulation of segmentation and segmental identity by Drosophila homeoproteins: the role of DNA binding in functional activity and specificity.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Evolutionary dynamics of the enhancer region of even-skipped in Drosophila.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

The Drosophila gene tailless is expressed at the embryonic termini and is a member of the steroid receptor superfamily

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Pattern formation under the control of the terminal system in the Drosophila embryo

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Concentration-dependent transcriptional activation or repression by Krüppel from a single binding site

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Spatial control of the gap gene knirps in the Drosophila embryo by posterior morphogen system

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Biological function of unannotated transcription during the early development of Drosophila melanogaster

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

REDfly: a Regulatory Element Database for Drosophila.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Adaptive evolution of non-coding DNA in Drosophila

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Eve and ftz regulate a wide array of genes in blastoderm embryos: the selector homeoproteins directly or indirectly regulate most genes in Drosophila

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Silencers and domains of generalized repression

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2235902

Reductive amination for solid-phase coupling of protein. A practical alternative to cyanogen bromide

29 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18271625

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Chromatin structure mapping in vivo using methyltransferases

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18271625

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The general affinity of lac repressor for E. coli DNA: Implications for gene regulation in procaryotes and eucaryotes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18271625

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PBIO.0060027

1 reference

858769

858769

1 reference

1 reference

1 reference