Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse (Q42594046)

3 November 2017

Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse (English)

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3 November 2017

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7

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3 November 2017

9

Saurabh Sinha

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3 November 2017

6

Gene E Robinson

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3 November 2017

Miriam R Kantorovitz

1

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3 November 2017

Majid Kazemian

2

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3 November 2017

Sarah Kinston

3

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3 November 2017

Diego Miranda-Saavedra

4

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3 November 2017

Qiyun Zhu

5

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3 November 2017

Marc S Halfon

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3 November 2017

language of work or name

English

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publication date

1 October 2009

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3 November 2017

12

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based on heuristic

inferred from page(s)

published in

Developmental Cell

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3 November 2017

17

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3 November 2017

4

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3 November 2017

568-579

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ChIP-seq accurately predicts tissue-specific activity of enhancers

3 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

BloodExpress: a database of gene expression in mouse haematopoiesis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Tissue-specific regulatory elements in mammalian promoters

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Predicting tissue-specific enhancers in the human genome

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

In vivo enhancer analysis of human conserved non-coding sequences

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Endoglin expression in the endothelium is regulated by Fli-1, Erg, and Elf-1 acting on the promoter and a -8-kb enhancer

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Using hexamers to predict cis-regulatory motifs in Drosophila.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Fli1, Elf1, and Ets1 regulate the proximal promoter of the LMO2 gene in endothelial cells.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Modulefinder: a tool for computational discovery of cis regulatory modules

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Assessing computational tools for the discovery of transcription factor binding sites

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Transcriptional control in the segmentation gene network of Drosophila

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Detection of functional DNA motifs via statistical over-representation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Cluster-Buster: Finding dense clusters of motifs in DNA sequences.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

TRANSFAC: transcriptional regulation, from patterns to profiles

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

A statistical method for finding transcription factor binding sites.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Lineage commitment in lymphopoiesis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Tandem repeats finder: a program to analyze DNA sequences

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

The hardwiring of development: organization and function of genomic regulatory systems.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

A statistical method for alignment-free comparison of regulatory sequences.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

A probabilistic method to detect regulatory modules.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

Characterization of a novel subset of cardiac cells and their progenitors in the Drosophila embryo.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2768654

TFBScluster: a resource for the characterization of transcriptional regulatory networks

16 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19853570

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.DEVCEL.2009.09.002

1 reference

3 November 2017

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3 November 2017

1 reference