(Q33588536)

28 July 2017

title

A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells (English)

1 reference

28 July 2017

1 reference

1 reference

Hedi Peterson

2

0 references

Pascal Kahlem

Pascal Kahlem

4

0 references

Lukas Chavez

Lukas Chavez

3

0 references

Jaak Vilo

Jaak Vilo

6

0 references

Hans Lehrach

5

Hans Lehrach

1 reference

28 July 2017

7

James Adjaye

1 reference

28 July 2017

Marc Jung

1

1 reference

28 July 2017

language of work or name

English

0 references

publication date

21 May 2010

1 reference

28 July 2017

1 reference

28 July 2017

volume

5

1 reference

28 July 2017

issue

5

1 reference

28 July 2017

page(s)

e10709

1 reference

Creative Commons Attribution 4.0 International

28 July 2017

copyright license

start time

21 May 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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A general mechanism for transcription regulation by Oct1 and Oct4 in response to genotoxic and oxidative stress

21 June 2018

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

21 June 2018

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Cdk2ap1 is required for epigenetic silencing of Oct4 during murine embryonic stem cell differentiation

21 June 2018

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The molecular basis of genistein-induced mitotic arrest and exit of self-renewal in embryonal carcinoma and primary cancer cell lines

21 June 2018

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Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET

21 June 2018

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Msx1 and Msx2 are required for endothelial-mesenchymal transformation of the atrioventricular cushions and patterning of the atrioventricular myocardium

21 June 2018

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

21 June 2018

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Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data.

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

21 June 2018

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Islet-1: a potentially important role for an islet cell gene in visceral fat.

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes

21 June 2018

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

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

The stem cell identity of testicular cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Developmental pluripotency-associated 4 (DPPA4) localized in active chromatin inhibits mouse embryonic stem cell differentiation into a primitive ectoderm lineage

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Model-based analysis of two-color arrays (MA2C).

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Silencing of core transcription factors in human EC cells highlights the importance of autocrine FGF signaling for self-renewal

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Anaphase initiation is regulated by antagonistic ubiquitination and deubiquitination activities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Qualification of embryonal carcinoma 2102Ep as a reference for human embryonic stem cell research.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Dissecting Oct3/4-regulated gene networks in embryonic stem cells by expression profiling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Molecular control of pluripotency

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Dissecting self-renewal in stem cells with RNA interference

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Embryonic stem (ES) cells and embryonal carcinoma (EC) cells: opposite sides of the same coin.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Core transcriptional regulatory circuitry in human embryonic stem cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Primary differentiation in the human blastocyst: comparative molecular portraits of inner cell mass and trophectoderm cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Oct-3/4 maintains the proliferative embryonic stem cell state via specific binding to a variant octamer sequence in the regulatory region of the UTF1 locus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Transcriptional regulation of nanog by OCT4 and SOX2.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

p53 induces differentiation of mouse embryonic stem cells by suppressing Nanog expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

A novel, high-performance random array platform for quantitative gene expression profiling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Bioconductor: open software development for computational biology and bioinformatics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

21 June 2018

An overview of Ensembl

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Human STELLAR, NANOG, and GDF3 genes are expressed in pluripotent cells and map to chromosome 12p13, a hotspot for teratocarcinoma

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

DAVID: Database for Annotation, Visualization, and Integrated Discovery

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

CR6-interacting factor 1 interacts with Gadd45 family proteins and modulates the cell cycle

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Fbx15 is a novel target of Oct3/4 but is dispensable for embryonic stem cell self-renewal and mouse development

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

TRANSFAC: transcriptional regulation, from patterns to profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Synergism with the coactivator OBF-1 (OCA-B, BOB-1) is mediated by a specific POU dimer configuration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Activators and target genes of Rel/NF-kappaB transcription factors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

The CNC basic leucine zipper factor, Nrf1, is essential for cell survival in response to oxidative stress-inducing agents. Role for Nrf1 in gamma-gcs(l) and gss expression in mouse fibroblasts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Developmental expression of specific genes detected in high-quality cDNA libraries from single human preimplantation embryos

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

The gene for the embryonic stem cell coactivator UTF1 carries a regulatory element which selectively interacts with a complex composed of Oct-3/4 and Sox-2.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

New POU dimer configuration mediates antagonistic control of an osteopontin preimplantation enhancer by Oct-4 and Sox-2

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Targeted disruption of the ubiquitous CNC-bZIP transcription factor, Nrf-1, results in anemia and embryonic lethality in mice

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Synergistic activation of the fibroblast growth factor 4 enhancer by Sox2 and Oct-3 depends on protein-protein interactions facilitated by a specific spatial arrangement of factor binding sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

A dynamic balance between ARP-1/COUP-TFII, EAR-3/COUP-TFI, and retinoic acid receptor:retinoid X receptor heterodimers regulates Oct-3/4 expression in embryonal carcinoma cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Retinoic acid-induced differentiation of the developmentally pluripotent human germ cell tumor-derived cell line, NCCIT.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Octamer binding proteins confer transcriptional activity in early mouse embryogenesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

The transcription factor LF-A1 interacts with a bipartite recognition sequence in the promoter regions of several liver-specific genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Basic principles of ROC analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

Genetic engineering of human embryonic stem cells with lentiviral vectors

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010709

Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010709

Identification of genes expressed in human primordial germ cells at the time of entry of the female germ line into meiosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010709

Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010709

TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010709

Octamer and Sox elements are required for transcriptional cis regulation of Nanog gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010709

REST selectively represses a subset of RE1-containing neuronal genes in mouse embryonic stem cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010709

Ebf gene function is required for coupling neuronal differentiation and cell cycle exit

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010709

Pax5 determines B- versus T-cell fate and does not block early myeloid-lineage development.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010709

Use of within-array replicate spots for assessing differential expression in microarray experiments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010709

Control of early fate decisions in human ES cells by distinct states of TGFbeta pathway activity

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2873957

10.1371/JOURNAL.PONE.0010709

31 October 2018

Identifiers

DOI

1 reference

28 July 2017

0 references

1 reference

28 July 2017

1 reference