(Q37273674)

English

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships

scientific article published on 29 May 2009

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scholarly article

1 reference

Europe PubMed Central

19 August 2017

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships (English)

1 reference

Europe PubMed Central

19 August 2017

cis-regulatory element

1 reference

based on heuristic

inferred from title

2

object named as

Uwe Ohler

1 reference

Europe PubMed Central

19 August 2017

3

object named as

Gregory A Wray

1 reference

Europe PubMed Central

19 August 2017

author name string

Ken Daigoro Yokoyama

1

1 reference

Europe PubMed Central

19 August 2017

language of work or name

0 references

publication date

29 May 2009

1 reference

Europe PubMed Central

19 August 2017

Nucleic Acids Research

1 reference

Europe PubMed Central

19 August 2017

37

1 reference

Europe PubMed Central

19 August 2017

13

1 reference

Europe PubMed Central

19 August 2017

e92

1 reference

Europe PubMed Central

19 August 2017

Poly(dA:dT) tracts: major determinants of nucleosome organization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

The DNA-encoded nucleosome organization of a eukaryotic genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Computational structural analysis: multiple proteins bound to DNA

1 reference

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p53-Induced DNA bending: the interplay between p53-DNA and p53-p53 interactions

1 reference

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6 September 2017

The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site

1 reference

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6 September 2017

MEF2: a central regulator of diverse developmental programs

1 reference

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6 September 2017

Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1

1 reference

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6 September 2017

Large-scale discovery of promoter motifs in Drosophila melanogaster

1 reference

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Serum response factor binding sites differ in three human cell types

1 reference

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6 September 2017

Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters

1 reference

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6 September 2017

Serum response factor: master regulator of the actin cytoskeleton and contractile apparatus

1 reference

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6 September 2017

Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters

1 reference

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6 September 2017

Comparative genomics of Drosophila and human core promoters

1 reference

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6 September 2017

Genome-wide analysis of mammalian promoter architecture and evolution

1 reference

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6 September 2017

Alignments anchored on genomic landmarks can aid in the identification of regulatory elements

1 reference

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6 September 2017

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

1 reference

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6 September 2017

Assessing computational tools for the discovery of transcription factor binding sites

1 reference

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6 September 2017

The expression of the human neuronal alpha3 Na+,K+-ATPase subunit gene is regulated by the activity of the Sp1 and NF-Y transcription factors

1 reference

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6 September 2017

Clustering of DNA sequences in human promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

The UCSC Table Browser data retrieval tool

1 reference

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6 September 2017

Computational detection of cis -regulatory modules.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Homeobox genes: a molecular link between development and cancer.

1 reference

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6 September 2017

YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

The evolution of transcriptional regulation in eukaryotes

1 reference

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6 September 2017

Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells

1 reference

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6 September 2017

TRANSFAC: transcriptional regulation, from patterns to profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Initial sequencing and comparative analysis of the mouse genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Serum response factor: discovery, biochemistry, biological roles and implications for tissue injury healing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Identifying regulatory networks by combinatorial analysis of promoter elements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

A polymorphic dinucleotide repeat in the rat nucleolin gene forms Z-DNA and inhibits promoter activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

DNA bending by an adenine-thymine tract and its role in gene regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Initial sequencing and analysis of the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

RefSeq and LocusLink: NCBI gene-centered resources

1 reference

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6 September 2017

Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis

1 reference

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6 September 2017

Solution structure of the MEF2A-DNA complex: structural basis for the modulation of DNA bending and specificity by MADS-box transcription factors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Discovering regulatory elements in non-coding sequences by analysis of spaced dyads

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

NCBI's LocusLink and RefSeq

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Identification of proteins that interact with NF-YA

1 reference

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6 September 2017

The biology of eukaryotic promoter prediction--a review

1 reference

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6 September 2017

Systematic determination of genetic network architecture

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure

1 reference

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6 September 2017

MADS-box transcription factors adopt alternative mechanisms for bending DNA.

1 reference

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6 September 2017

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Interaction of ATF6 and serum response factor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Recruitment of the tinman homolog Nkx-2.5 by serum response factor activates cardiac alpha-actin gene transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Physical interaction between the mitogen-responsive serum response factor and myogenic basic-helix-loop-helix proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Cooperative binding of an Ultrabithorax homeodomain protein to nearby and distant DNA sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

Direct recognition of initiator elements by a component of the transcription factor IID complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

YY1 facilitates the association of serum response factor with the c-fos serum response element

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715254

6 September 2017

TATA-binding protein-associated factor(s) in TFIID function through the initiator to direct basal transcription from a TATA-less class II promoter.

1 reference

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6 September 2017

The chemistry and biology of left-handed Z-DNA.

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6 September 2017

Comparison of the consensus sequence flanking translational start sites in Drosophila and vertebrates

1 reference

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6 September 2017

The role of DNA-binding proteins in differentiation and transformation.

1 reference

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6 September 2017

Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences

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6 September 2017

Intrinsically bent DNA.

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6 September 2017

Homeogenes in mammalian development and the evolution of the cranium and central nervous system

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6 September 2017

DNA curving and bending in protein-DNA recognition

1 reference

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6 September 2017

Predicting transcription factor synergism

1 reference

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14 September 2017

d(TG)n.d(CA)n sequences upstream of the rat prolactin gene form Z-DNA and inhibit gene transcription

1 reference

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14 September 2017

Statistical analyses of counts and distributions of restriction sites in DNA sequences

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14 September 2017

Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes

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28 September 2017

STAMP: a web tool for exploring DNA-binding motif similarities

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26 June 2018

Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation

1 reference

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26 June 2018

ERK2- and p90(Rsk2)-dependent pathways regulate the CCAAT/enhancer-binding protein-beta interaction with serum response factor

1 reference

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26 June 2018

Regulatory element detection using correlation with expression.

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26 June 2018

Protein-DNA interactions: A structural analysis

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26 June 2018

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

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26 June 2018

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26 June 2018

A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha.

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3 September 2018

Predicting polymerase II core promoters by cooperating transcription factor binding sites in eukaryotic genes.

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3 September 2018

Regulatory motif finding by logic regression

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3 September 2018

Predicting gene expression from sequence

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3 September 2018

Immunity regulatory DNAs share common organizational features in Drosophila

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3 September 2018

Identification of regulatory elements using a feature selection method.

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3 September 2018

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.

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3 September 2018

Transcriptional cooperativity: bending over backwards and doing the flip.

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3 September 2018

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3 December 2018

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3 December 2018

Eukaryotic transcription factors

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The role of the transcription bubble and TFIIB in promoter clearance by RNA polymerase II

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https://pubmed.ncbi.nlm.nih.gov/19483094

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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https://pubmed.ncbi.nlm.nih.gov/19483094

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Role of core promoter structure in assembly of the RNA polymerase II preinitiation complex. A common pathway for formation of preinitiation intermediates at many TATA and TATA-less promoters

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

NF-Y binding to twin CCAAT boxes: role of Q-rich domains and histone fold helices

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https://pubmed.ncbi.nlm.nih.gov/19483094

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKP423

1 reference

Europe PubMed Central

19 August 2017

1 reference

Europe PubMed Central

19 August 2017

1 reference

Europe PubMed Central

19 August 2017

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0 references

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