(Q35560754)

English

Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling

scientific article published on 13 February 2015

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scholarly article

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Europe PubMed Central

PubMed publication ID

8 August 2017

Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling (English)

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Europe PubMed Central

PubMed publication ID

8 August 2017

Kristofer Davie

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Kristofer Davie

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Jelle Jacobs

2

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Mardelle Atkins

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Mardelle Atkins

3

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Delphine Potier

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Delphine Potier

4

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Georg Halder

6

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Stein Aerts

7

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Valerie Christiaens

5

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Valerie Christiaens

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Europe PubMed Central

PubMed publication ID

8 August 2017

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13 February 2015

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Europe PubMed Central

PubMed publication ID

8 August 2017

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Europe PubMed Central

PubMed publication ID

8 August 2017

11

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Europe PubMed Central

PubMed publication ID

8 August 2017

2

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

e1004994

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Europe PubMed Central

PubMed publication ID

8 August 2017

copyright license

Creative Commons Attribution 4.0 International

13 February 2015

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April 2022 Public Data File from Crossref

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Europe PubMed Central

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4334524/fullTextXML

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limma

2 references

Europe PubMed Central

22 June 2022

https://europepmc.org/article/PMC/4334524

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inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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DESeq2

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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affy

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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GEOquery

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

HTSeq--a Python framework to work with high-throughput sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

iRegulon: from a gene list to a gene regulatory network using large motif and track collections

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

An atlas of active enhancers across human cell types and tissues

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Transcriptional enhancers: from properties to genome-wide predictions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

FlyBase 102--advanced approaches to interrogating FlyBase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

A common set of DNA regulatory elements shapes Drosophila appendages

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Evidence for tissue-specific Jak/STAT target genes in Drosophila optic lobe development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Retinal differentiation in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Developmental fate and cellular maturity encoded in human regulatory DNA landscapes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

The BTB-zinc finger transcription factor abrupt acts as an epithelial oncogene in Drosophila melanogaster through maintaining a progenitor-like cell state

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Drosophila melanogaster: a model and a tool to investigate malignancy and identify new therapeutics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

In Drosophila, RhoGEF2 cooperates with activated Ras in tumorigenesis through a pathway involving Rho1-Rok-Myosin-II and JNK signalling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

The actin cross-linker Filamin/Cheerio mediates tumor malignancy downstream of JNK signaling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

A GAL4-driver line resource for Drosophila neurobiology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

The accessible chromatin landscape of the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

An integrated encyclopedia of DNA elements in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Functions of DNA methylation: islands, start sites, gene bodies and beyond

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Fast gapped-read alignment with Bowtie 2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Transcriptional control of cell fate specification: lessons from the fly retina.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Computational strategies for the genome-wide identification of cis-regulatory elements and transcriptional targets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Loss of the Drosophila cell polarity regulator Scribbled promotes epithelial tissue overgrowth and cooperation with oncogenic Ras-Raf through impaired Hippo pathway signaling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

STAT is an essential activator of the zygotic genome in the early Drosophila embryo.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Using MACS to identify peaks from ChIP-Seq data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Retinal determination the beginning of eye development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

The NIH Roadmap Epigenomics Mapping Consortium

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Discovery and characterization of chromatin states for systematic annotation of the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

BigWig and BigBed: enabling browsing of large distributed datasets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Size matters: the contribution of cell proliferation to the progression of the specification Drosophila eye gene regulatory network

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Characterization of a dominant-active STAT that promotes tumorigenesis in Drosophila.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

chinmo is a functional effector of the JAK/STAT pathway that regulates eye development, tumor formation, and stem cell self-renewal in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

BEDTools: a flexible suite of utilities for comparing genomic features

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Interaction between Ras(V12) and scribbled clones induces tumour growth and invasion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

CEAS: cis-regulatory element annotation system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

The Sequence Alignment/Map format and SAMtools

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Genome-wide expression profiling in the Drosophila eye reveals unexpected repression of notch signaling by the JAK/STAT pathway

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

The TEAD/TEF family of transcription factor Scalloped mediates Hippo signaling in organ size control

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

ORegAnno: an open-access community-driven resource for regulatory annotation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

JNK- and Fos-regulated Mmp1 expression cooperates with Ras to induce invasive tumors in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

JAK/STAT signaling promotes regional specification by negatively regulating wingless expression in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Non-cell-autonomous induction of tissue overgrowth by JNK/Ras cooperation in a Drosophila tumor model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Genome-wide RNAi analysis of JAK/STAT signaling components in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

scribble mutants cooperate with oncogenic Ras or Notch to cause neoplastic overgrowth in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

A Genetic Screen in Drosophila for Metastatic Behavior

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

12 July 2018

Loss of cell polarity drives tumor growth and invasion through JNK activation in Drosophila.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1004994

21 January 2018

Ectopic expression of germline genes drives malignant brain tumor growth in Drosophila.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1004994

21 January 2018

Activation of JNK signaling links lgl mutations to disruption of the cell polarity and epithelial organization in Drosophila imaginal discs.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1004994

21 January 2018

Differential activities of the Drosophila JAK/STAT pathway ligands Upd, Upd2 and Upd3.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1004994

21 January 2018

Cloning and expression of Drosophila SOCS36E and its potential regulation by the JAK/STAT pathway.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1004994

21 January 2018

A gradient of JAK pathway activity patterns the anterior-posterior axis of the follicular epithelium.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1004994

21 January 2018

The endocytic control of JAK/STAT signalling in Drosophila.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1004994

21 January 2018

Dally cooperates with Drosophila Frizzled 2 to transduce Wingless signalling

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1004994

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1004994

21 January 2018

Drosophila atonal fully rescues the phenotype of Math1 null mice: new functions evolve in new cellular contexts.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1004994

21 January 2018

The maternal JAK/STAT pathway of Drosophila regulates embryonic dorsal-ventral patterning.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4334524

26 September 2018

Overexpression of TFIIB-related factor 2 is significantly correlated with tumor angiogenesis and poor survival in patients with esophageal squamous cell cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/25679813

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1371/JOURNAL.PGEN.1004994

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

ResearchGate publication ID

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