(Q36672362)

15 August 2017

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

1 reference

15 August 2017

4

Saurabh Sinha

1 reference

15 August 2017

3

Xin He

1 reference

15 August 2017

Long Li

1

1 reference

PMCID

2394749

15 August 2017

Qianqian Zhu

series ordinal

2

1 reference

PMCID

2394749

15 August 2017

Marc S Halfon

series ordinal

5

1 reference

15 August 2017

1 January 2007

1 reference

15 August 2017

1 reference

15 August 2017

8

1 reference

15 August 2017

R101

1 reference

15 August 2017

6

1 reference

https://scigraph.springernature.com/pub.10.1186/gb-2007-8-6-r101

15 August 2017

0 references

cites work

The evolutionary significance of cis-regulatory mutations

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Locus control region transcription plays an active role in long-range gene activation

30 September 2017

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Comparative genomics of Drosophila and human core promoters

30 September 2017

1 reference

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Close sequence comparisons are sufficient to identify human cis-regulatory elements.

30 September 2017

1 reference

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Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison

30 September 2017

1 reference

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Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells

30 September 2017

1 reference

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

30 September 2017

1 reference

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The interpretation of morphogen gradients

30 September 2017

1 reference

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Using hexamers to predict cis-regulatory motifs in Drosophila.

30 September 2017

1 reference

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The transcriptional landscape of the mammalian genome

30 September 2017

1 reference

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Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content

30 September 2017

1 reference

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A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription

30 September 2017

1 reference

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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

30 September 2017

1 reference

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Detecting novel low-abundant transcripts in Drosophila

30 September 2017

1 reference

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Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

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

30 September 2017

1 reference

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The identification and functional characterisation of conserved regulatory elements in developmental genes

30 September 2017

1 reference

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Computational methods for transcriptional regulation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Highly conserved non-coding sequences are associated with vertebrate development

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Whole-genome analysis of temporal gene expression during foregut development

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Transcriptional control in the segmentation gene network of Drosophila

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Applied bioinformatics for the identification of regulatory elements

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Ultraconserved Elements in the Human Genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

The regulatory content of intergenic DNA shapes genome architecture

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Coordinate enhancers share common organizational features in the Drosophila genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Analysis of intergenic transcription in the human IL-4/IL-13 gene cluster

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Benchmarking tools for the alignment of functional noncoding DNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Computational prediction of transcription-factor binding site locations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Dissecting the transcription networks of a cell using computational genomics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Conservation of regulatory elements between two species of Drosophila

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Empirical analysis of transcriptional activity in the Arabidopsis genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Highly restricted localization of RNA polymerase II within a locus control region of a tissue-specific chromatin domain

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Homotypic regulatory clusters in Drosophila.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

The RNA polymerase II core promoter

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Phylogenetic shadowing of primate sequences to find functional regions of the human genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

The transcriptional activity of human Chromosome 22

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Chromatin remodeling and extragenic transcription at the MHC class II locus control region.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Transcription defines the embryonic domains of cis-regulatory activity at the Drosophila bithorax complex

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Exploring genetic regulatory networks in metazoan development: methods and models

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Molecular mechanisms of selector gene function and evolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Site clustering over random expectation.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Large-scale transcriptional activity in chromosomes 21 and 22

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

A genomic regulatory network for development

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

A predictive model for regulatory sequences directing liver-specific transcription.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

A statistical method for finding transcription factor binding sites.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Conserved noncoding sequences are reliable guides to regulatory elements.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Evidence for stabilizing selection in a eukaryotic enhancer element.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Tandem repeats finder: a program to analyze DNA sequences

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Intergenic transcription and transinduction of the human beta-globin locus

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Codon usage bias and base composition of nuclear genes in Drosophila

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Intergenic transcription through a polycomb group response element counteracts silencing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Turnover of binding sites for transcription factors involved in early Drosophila development.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Dpp signaling thresholds in the dorsal ectoderm of the Drosophila embryo

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Structure and evolution of a pair-rule interaction element: runt regulatory sequences in D. melanogaster and D. virilis.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Identification of regulatory regions which confer muscle-specific gene expression.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

High intrinsic rate of DNA loss in Drosophila.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Disperse versus compact elements for the regulation of runt stripes in Drosophila.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Determination of spatial domains of zygotic gene expression in the Drosophila embryo by the affinity of binding sites for the bicoid morphogen.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Biological code breaking in the 21st century

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Conservation patterns in different functional sequence categories of divergent Drosophila species.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

REDfly: a Regulatory Element Database for Drosophila.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Lateral inhibition in proneural clusters: cis-regulatory logic and default repression by Suppressor of Hairless

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

A gene expression map for the euchromatic genome of Drosophila melanogaster.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

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

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Predicting gene expression from sequence.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Immunity regulatory DNAs share common organizational features in Drosophila

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

A probabilistic method to detect regulatory modules.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Human-mouse genome comparisons to locate regulatory sites

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Two distinct mechanisms for long-range patterning by Decapentaplegic in the Drosophila wing.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

The gradient morphogen bicoid is a concentration-dependent transcriptional activator.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2394749

Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences

20 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17550599

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

(Re)modeling the transcriptional enhancer

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17550599

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/GB-2007-8-6-R101

1 reference

15 August 2017

1 reference

15 August 2017

1 reference

PMCID

2394749