Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity (Q34027627)

30 July 2017

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity (English)

1 reference

30 July 2017

22

1 reference

30 July 2017

26

1 reference

30 July 2017

10

Damian Keefe

0 references

Nathan C. Sheffield

Nathan C Sheffield

7

0 references

Alan P. Boyle

Alan P Boyle

4

0 references

Debbie Winter

Deborah Winter

19

0 references

Mikael Huss

Mikael Huss

9

0 references

Darin London

12

Darin London

1 reference

30 July 2017

24

Gregory E Crawford

1 reference

30 July 2017

8

Stefan Gräf

1 reference

30 July 2017

1

Lingyun Song

1 reference

30 July 2017

25

Jason D Lieb

1 reference

30 July 2017

23

Vishwanath R Iyer

1 reference

30 July 2017

Zhancheng Zhang

2

1 reference

30 July 2017

Linda L Grasfeder

3

1 reference

30 July 2017

Paul G Giresi

5

1 reference

30 July 2017

Bum-Kyu Lee

6

1 reference

30 July 2017

Zheng Liu

11

1 reference

30 July 2017

Ryan M McDaniell

13

1 reference

30 July 2017

Yoichiro Shibata

14

1 reference

30 July 2017

Kimberly A Showers

15

1 reference

30 July 2017

Jeremy M Simon

16

1 reference

30 July 2017

Teresa Vales

17

1 reference

30 July 2017

Tianyuan Wang

18

1 reference

30 July 2017

Zhuzhu Zhang

20

1 reference

30 July 2017

Neil D Clarke

21

1 reference

30 July 2017

12 July 2011

1 reference

30 July 2017

1 reference

30 July 2017

21

1 reference

30 July 2017

10

1 reference

30 July 2017

1757-1767

1 reference

A user's guide to the encyclopedia of DNA elements (ENCODE)

30 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Structure and function of active chromatin and DNase I hypersensitive sites.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

A unique chromatin signature uncovers early developmental enhancers in humans

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Genomics tools for unraveling chromosome architecture

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

The Gerbich blood group system: a review.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Heritable individual-specific and allele-specific chromatin signatures in humans

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Evidence-ranked motif identification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Close association of RNA polymerase II and many transcription factors with Pol III genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Integrated approach for the identification of human hepatocyte nuclear factor 4alpha target genes using protein binding microarrays

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

hPDI: a database of experimental human protein-DNA interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Exhaustive search for over-represented DNA sequence motifs with CisFinder

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

F-Seq: a feature density estimator for high-throughput sequence tags

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Database resources of the National Center for Biotechnology Information

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Nucleosome and transcription activator antagonism at human beta-globin locus control region DNase I hypersensitive sites

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

A chromatin landmark and transcription initiation at most promoters in human cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Distant regulatory elements in a Sox10-beta GEO BAC transgene are required for expression of Sox10 in the enteric nervous system and other neural crest-derived tissues.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Interchromosomal associations between alternatively expressed loci

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

The human genome browser at UCSC

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

A distant upstream promoter of the HNF-4alpha gene connects the transcription factors involved in maturity-onset diabetes of the young

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

IRF family of transcription factors as regulators of host defense

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Functional AP1 and CRE response elements in the human keratinocyte transglutaminase promoter mediating Whn suppression

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

The protein CTCF is required for the enhancer blocking activity of vertebrate insulators

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

The orphan receptors COUP-TF and HNF-4 serve as accessory factors required for induction of phosphoenolpyruvate carboxykinase gene transcription by glucocorticoids

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Nuclease hypersensitive sites in chromatin

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Mapping and analysis of chromatin state dynamics in nine human cell types

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Role of redox signaling regulation in propyl gallate-induced apoptosis of human leukemia cells

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

A map of open chromatin in human pancreatic islets

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip).

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Mapping short DNA sequencing reads and calling variants using mapping quality scores

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

29 October 2018

GATA1-related leukaemias

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Foxs and Ets in the transcriptional regulation of endothelial cell differentiation and angiogenesis

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

29 October 2018

Identifiers

DOI

10.1101/GR.121541.111

1 reference

30 July 2017

1 reference

30 July 2017

1 reference