(Q30618656)

17 August 2017

Models incorporating chromatin modification data identify functionally important p53 binding sites (English)

1 reference

17 August 2017

Ji-Hyun Lim

1

1 reference

17 August 2017

Richard D Iggo

series ordinal

2

1 reference

17 August 2017

Daniel Barker

series ordinal

3

1 reference

17 August 2017

language of work or name

English

0 references

publication date

17 April 2013

1 reference

17 August 2017

Nucleic Acids Research

1 reference

17 August 2017

41

1 reference

17 August 2017

11

1 reference

17 August 2017

5582-5593

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

17 August 2017

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/3675478

based on heuristic

inferred from PubMed Central ID database lookup

cites work

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20 June 2018

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A map of the cis-regulatory sequences in the mouse genome

20 June 2018

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ATM and MET kinases are synthetic lethal with nongenotoxic activation of p53.

20 June 2018

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20 June 2018

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20 June 2018

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FIMO: scanning for occurrences of a given motif

20 June 2018

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A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology

20 June 2018

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A unique chromatin signature uncovers early developmental enhancers in humans

20 June 2018

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

20 June 2018

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The UCSC Genome Browser database: update 2011

20 June 2018

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Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

20 June 2018

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

20 June 2018

1 reference

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Genome-wide prediction of transcription factor binding sites using an integrated model.

20 June 2018

1 reference

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An oestrogen-receptor-α-bound human chromatin interactome

20 June 2018

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MEME SUITE: tools for motif discovery and searching

20 June 2018

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Blinded by the Light: The Growing Complexity of p53

20 June 2018

1 reference

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The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes

20 June 2018

1 reference

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

20 June 2018

1 reference

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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

20 June 2018

1 reference

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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

20 June 2018

1 reference

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Characterization of genome-wide p53-binding sites upon stress response.

20 June 2018

1 reference

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Transcriptional control of human p53-regulated genes

20 June 2018

1 reference

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Divergent evolution of human p53 binding sites: cell cycle versus apoptosis

20 June 2018

1 reference

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Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence

20 June 2018

1 reference

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Identifying tissue-selective transcription factor binding sites in vertebrate promoters

20 June 2018

1 reference

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Post-translational modification of p53 in tumorigenesis

20 June 2018

1 reference

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Ordered cooperative functions of PRMT1, p300, and CARM1 in transcriptional activation by p53

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

p53-mediated transcriptional activation: from test tube to cell

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

The human genome browser at UCSC

20 June 2018

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Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails

20 June 2018

1 reference

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BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes.

20 June 2018

1 reference

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Oncogenic mutations of the p53 tumor suppressor: the demons of the guardian of the genome.

20 June 2018

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

WAF1, a potential mediator of p53 tumor suppression

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

Interaction of p53 with its consensus DNA-binding site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

Mammalian p53 can function as a transcription factor in yeast

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

Definition of a consensus binding site for p53

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

ENCODE: The human encyclopaedia.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

OSCAR: one-class SVM for accurate recognition of cis-elements

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

MUSA: a parameter free algorithm for the identification of biologically significant motifs.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

A solution to the problem of separation in logistic regression.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

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

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3675478

25 November 2018

Identifiers

DOI

10.1093/NAR/GKT260

1 reference

17 August 2017

1 reference

17 August 2017

PubMed publication ID

23599002

1 reference