Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment (Q30830996)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

title

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

Anthony Mathelier

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

Luis del Peso

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

author name string

Rebecca Worsley Hunt

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

language of work or name

English

0 references

publication date

13 June 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

volume

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

page(s)

472

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json

Widespread misinterpretable ChIP-seq bias in yeast

20 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Modulation of gene expression via overlapping binding sites exerted by ZNF143, Notch1 and THAP11

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

DNA-binding specificities of human transcription factors

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

ENCODE data in the UCSC Genome Browser: year 5 update

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

An integrated encyclopedia of DNA elements in the human genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

The UCSC genome browser and associated tools

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Inferring direct DNA binding from ChIP-seq

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Improved models for transcription factor binding site identification using nonindependent interactions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

The forkhead transcription factor FOXK2 promotes AP-1-mediated transcriptional regulation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Inferring transcription factor complexes from ChIP-seq data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

MEME-ChIP: motif analysis of large DNA datasets

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Theoretical and empirical quality assessment of transcription factor-binding motifs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Nrf2-ARE stress response mechanism: A control point in oxidative stress-mediated dysfunctions and chronic inflammatory diseases

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Deep and wide digging for binding motifs in ChIP-Seq data.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Evaluation of algorithm performance in ChIP-seq peak detection

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

MER41 repeat sequences contain inducible STAT1 binding sites

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

GREAT improves functional interpretation of cis-regulatory regions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Evidence-ranked motif identification

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Human DNA methylomes at base resolution show widespread epigenomic differences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Mapping accessible chromatin regions using Sono-Seq

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Distinguishing direct versus indirect transcription factor-DNA interactions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Biopython: freely available Python tools for computational molecular biology and bioinformatics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Asap: a framework for over-representation statistics for transcription factor binding sites

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

The long terminal repeat (LTR) of ERV-9 human endogenous retrovirus binds to NF-Y in the assembly of an active LTR enhancer complex NF-Y/MZF1/GATA-2.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Estrogen receptor-related receptor gamma has an exceptionally broad specificity of DNA sequence recognition.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

The UCSC Table Browser data retrieval tool

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

TFBS: Computational framework for transcription factor binding site analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

FLI1 and EWS-FLI1 function as ternary complex factors and ELK1 and SAP1a function as ternary and quaternary complex factors on the Egr1 promoter serum response elements

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Staf, a promiscuous activator for enhanced transcription by RNA polymerases II and III

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

RSAT 2011: regulatory sequence analysis tools.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612

Transposable B2 SINE elements can provide mobile RNA polymerase II promoters

25 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24927817

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A chromatin-modifying function of JNK during stem cell differentiation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24927817

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-15-472

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

20 March 2020

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1471-2164-15-472

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

PubMed publication ID

24927817

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json