(Q34193463)

31 July 2017

Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets (English)

1 reference

31 July 2017

1 reference

Wyeth W Wasserman

2

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author name string

Rebecca Worsley Hunt

series ordinal

1

1 reference

31 July 2017

29 July 2014

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31 July 2017

1 reference

31 July 2017

15

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31 July 2017

7

1 reference

31 July 2017

412

1 reference

Creative Commons Attribution 4.0 International

31 July 2017

start time

1 July 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1186/s13059-014-0412-4

1 reference

SciGraph

https://scigraph.springernature.com/pub.10.1186/s13059-014-0412-4

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

9 September 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Cohesin and polycomb proteins functionally interact to control transcription at silenced and active genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

ENCODE data in the UCSC Genome Browser: year 5 update

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

An integrated encyclopedia of DNA elements in the human genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

The UCSC genome browser and associated tools

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Inferring direct DNA binding from ChIP-seq

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Systematic evaluation of factors influencing ChIP-seq fidelity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

ChIP-Seq: technical considerations for obtaining high-quality data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Systematic bias in high-throughput sequencing data and its correction by BEADS.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Conserved, developmentally regulated mechanism couples chromosomal looping and heterochromatin barrier activity at the homeobox gene A locus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Mediator and cohesin connect gene expression and chromatin architecture

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Evaluation of algorithm performance in ChIP-seq peak detection

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

A CTCF-independent role for cohesin in tissue-specific transcription

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Computation for ChIP-seq and RNA-seq studies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Human DNA methylomes at base resolution show widespread epigenomic differences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Mapping accessible chromatin regions using Sono-Seq

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Impact of chromatin structures on DNA processing for genomic analyses

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Cohesins functionally associate with CTCF on mammalian chromosome arms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Cohesin mediates transcriptional insulation by CCCTC-binding factor

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Quantifying similarity between motifs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Repbase Update, a database of eukaryotic repetitive elements

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

TFBS: Computational framework for transcription factor binding site analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

Quantifying hopping and jumping in facilitated diffusion of DNA-binding proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165360

A chromatin-modifying function of JNK during stem cell differentiation

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25070602

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/PREACCEPT-1454983695127944

reason for deprecated rank

redirect

1 reference

PubMed ID

25070602

10.1186/S13059-014-0412-4

31 July 2017

1 reference

SciGraph

https://scigraph.springernature.com/pub.10.1186/s13059-014-0412-4

Dimensions Publication ID

9 September 2019

1 reference

https://scigraph.springernature.com/pub.10.1186/s13059-014-0412-4

release_3ug6pizvx5egpki5o54szc5wxa

9 September 2019

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/3ug6pizvx5egpki5o54szc5wxa

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMCID

4165360

1 reference

31 July 2017

1 reference

PubMed ID

25070602