Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices (Q35823685)

10 August 2017

Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices (English)

1 reference

10 August 2017

Jong Kyoung Kim

2

0 references

author name string

Young Min Oh

series ordinal

1

1 reference

10 August 2017

Seungjin Choi

series ordinal

3

1 reference

10 August 2017

Joo-Yeon Yoo

series ordinal

4

1 reference

10 August 2017

language of work or name

English

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publication date

19 December 2011

1 reference

10 August 2017

Nucleic Acids Research

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10 August 2017

40

1 reference

10 August 2017

5

1 reference

10 August 2017

e38

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

10 August 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

Cytoscape

1 reference

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

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Transcription factors ETF, E2F, and SP-1 are involved in cytokine-independent proliferation of murine hepatocytes.

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Ethanol-induced HO-1 and NQO1 are differentially regulated by HIF-1alpha and Nrf2 to attenuate inflammatory cytokine expression

11 July 2018

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Differential proteomics analysis reveals a role for E2F2 in the regulation of the Ahr pathway in T lymphocytes.

11 July 2018

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Integrating multiple evidence sources to predict transcription factor binding in the human genome

11 July 2018

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An atlas of combinatorial transcriptional regulation in mouse and man

11 July 2018

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ChIP-seq: advantages and challenges of a maturing technology

11 July 2018

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Prediction and experimental validation of novel STAT3 target genes in human cancer cells

11 July 2018

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Insights from genomic profiling of transcription factors

11 July 2018

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Distinguishing direct versus indirect transcription factor-DNA interactions

11 July 2018

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Diversity and complexity in DNA recognition by transcription factors

11 July 2018

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Histone modifications at human enhancers reflect global cell-type-specific gene expression

11 July 2018

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8-Chloro-adenosine-induced E2F1 promotes p14ARF gene activation in H1299 cells through displacing Sp1 from multiple overlapping E2F1/Sp1 sites

11 July 2018

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Requirement for chromatin-remodeling complex in novel tumor suppressor HIC1-mediated transcriptional repression and growth control

11 July 2018

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High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites

11 July 2018

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Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells

11 July 2018

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Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

11 July 2018

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MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs

11 July 2018

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Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site

11 July 2018

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Integration of external signaling pathways with the core transcriptional network in embryonic stem cells

11 July 2018

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Eukaryotic transcription factor binding sites--modeling and integrative search methods

11 July 2018

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FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription

11 July 2018

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High-resolution mapping and characterization of open chromatin across the genome

11 July 2018

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A nucleosome-guided map of transcription factor binding sites in yeast

11 July 2018

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An Atomic Model of the Interferon-β Enhanceosome

11 July 2018

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

11 July 2018

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11 July 2018

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11 July 2018

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Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues

11 July 2018

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Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae

11 July 2018

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TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

11 July 2018

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11 July 2018

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oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes

11 July 2018

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MatInspector and beyond: promoter analysis based on transcription factor binding sites

11 July 2018

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The E2F transcriptional network: old acquaintances with new faces

11 July 2018

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A common set of gene regulatory networks links metabolism and growth inhibition

11 July 2018

1 reference

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Biological control through regulated transcriptional coactivators

11 July 2018

1 reference

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Transcriptional regulatory code of a eukaryotic genome

11 July 2018

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11 July 2018

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Computational detection of cis -regulatory modules.

11 July 2018

1 reference

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Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.

11 July 2018

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MATCH: A tool for searching transcription factor binding sites in DNA sequences

11 July 2018

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Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences

11 July 2018

1 reference

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Specificity of gene regulation

11 July 2018

1 reference

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AP-1 as a regulator of cell life and death

11 July 2018

1 reference

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Signal Transduction and the Control of Gene Expression

11 July 2018

1 reference

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Close encounters of many kinds: Fos-Jun interactions that mediate transcription regulatory specificity.

11 July 2018

1 reference

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DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with natural target sites

11 July 2018

1 reference

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Transcription factors of the Sp1 family: interaction with E2F and regulation of the murine thymidine kinase promoter

11 July 2018

1 reference

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STAT3 is required for the gp130-mediated full activation of the c-myc gene

11 July 2018

1 reference

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The human POLD1 gene. Identification of an upstream activator sequence, activation by Sp1 and Sp3, and cell cycle regulation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3300004

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3300004

Functional erythroid promoters created by interaction of the transcription factor GATA-1 with CACCC and AP-1/NFE-2 elements

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3300004

Specific interaction between E2F1 and Sp1 regulates the expression of murine CTP:phosphocholine cytidylyltransferase alpha during the S phase

11 July 2018

1 reference

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The transcription factor Egr-1 is a regulator of the human TopBP1 gene.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3300004

On the power of profiles for transcription factor binding site detection.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3300004

Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3300004

Human-mouse genome comparisons to locate regulatory sites

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3300004

Sterol regulation of 3-hydroxy-3-methylglutaryl-coenzyme A synthase gene through a direct interaction between sterol regulatory element binding protein and the trimeric CCAAT-binding factor/nuclear factor Y.

24 September 2018

1 reference

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Cytoscape: a community-based framework for network modeling

24 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22187154

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKR1252

1 reference

release_3c4pgt64hbhbfcfr3kwdouymwq

10 August 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/3c4pgt64hbhbfcfr3kwdouymwq

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

10 August 2017

1 reference