Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia (Q38275870)

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English	Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia	scientific article

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia (English)

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

author name string

Li Wei Chang

1

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

Jacqueline E Payton

2

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

Wenlin Yuan

3

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

Timothy J Ley

4

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

Rakesh Nagarajan

5

1 reference

Europe PubMed Central

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1 September 2017

Gary D Stormo

6

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Europe PubMed Central

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1 September 2017

publication date

21 February 2008

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Europe PubMed Central

PMC publication ID

1 September 2017

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

9

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Europe PubMed Central

PMC publication ID

1 September 2017

2

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

R38

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis

1 reference

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6 September 2017

A core transcriptional network for early mesoderm development in Drosophila melanogaster

1 reference

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6 September 2017

Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria

1 reference

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Inferring gene regulatory networks from time series data using the minimum description length principle

1 reference

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6 September 2017

A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles.

1 reference

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6 September 2017

Bayesian sparse hidden components analysis for transcription regulation networks

1 reference

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6 September 2017

EVI1 and hematopoietic disorders: history and perspectives

1 reference

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A bi-dimensional regression tree approach to the modeling of gene expression regulation

1 reference

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Identifying the conserved network of cis-regulatory sites of a eukaryotic genome

1 reference

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Reverse engineering of regulatory networks in human B cells

1 reference

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A statistical method for constructing transcriptional regulatory networks using gene expression and sequence data

1 reference

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Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

1 reference

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Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation

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An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression

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6 September 2017

Transcriptional regulatory code of a eukaryotic genome

1 reference

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6 September 2017

Combined analysis of expression data and transcription factor binding sites in the yeast genome

1 reference

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6 September 2017

The leukemic fusion gene AML1-MDS1-EVI1 suppresses CEBPA in acute myeloid leukemia by activation of Calreticulin

1 reference

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6 September 2017

A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data

1 reference

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A ternary complex of transcription factors, Nishéd and NFATc4, and co-activator p300 bound to an intronic sequence, intronic regulatory element, is pivotal for the up-regulation of myosin light chain-2v gene in cardiac hypertrophy

1 reference

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Inferring quantitative models of regulatory networks from expression data

1 reference

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6 September 2017

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data

1 reference

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6 September 2017

Aligning multiple genomic sequences with the threaded blockset aligner

1 reference

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Control of pancreas and liver gene expression by HNF transcription factors

1 reference

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Tumor necrosis factor alpha activates the human plasminogen activator inhibitor-1 gene through a distal nuclear factor kappaB site.

1 reference

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6 September 2017

Ectopic expression of the homeobox gene Cdx2 is the transforming event in a mouse model of t(12;13)(p13;q12) acute myeloid leukemia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Identification and characterization of multi-species conserved sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Inferring genetic networks and identifying compound mode of action via expression profiling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling

1 reference

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Disruption of differentiation in human cancer: AML shows the way.

1 reference

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6 September 2017

TRANSFAC: transcriptional regulation, from patterns to profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Transcriptional regulatory networks in Saccharomyces cerevisiae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Transcriptional regulation of granulocyte and monocyte development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

rVista for comparative sequence-based discovery of functional transcription factor binding sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Reverse engineering gene networks using singular value decomposition and robust regression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Spi-B can functionally replace PU.1 in myeloid but not lymphoid development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Microarray analysis of eosinophils reveals a number of candidate survival and apoptosis genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Significance analysis of microarrays applied to the ionizing radiation response

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Cell-cycle-dependent activation of mitogen-activated protein kinase kinase (MEK-1/2) in myeloid leukemia cell lines and induction of growth inhibition and apoptosis by inhibitors of RAS signaling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Early growth response gene 1 stimulates development of hematopoietic progenitor cells along the macrophage lineage at the expense of the granulocyte and erythroid lineages

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Hematopoietic expression of HOXB4 is regulated in normal and leukemic stem cells through transcriptional activation of the HOXB4 promoter by upstream stimulating factor (USF)-1 and USF-2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Fusion proteins of the retinoic acid receptor-alpha recruit histone deacetylase in promyelocytic leukaemia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Analysis of E-box DNA binding during myeloid differentiation reveals complexes that contain Mad but not Max.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Octamer binding factors and their coactivator can activate the murine PU.1 (spi-1) promoter.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

The PML-retinoic acid receptor alpha translocation converts the receptor from an inhibitor to a retinoic acid-dependent activator of transcription factor AP-1

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Nerve growth factor induces transcription of transforming growth factor-beta 1 through a specific promoter element in PC12 cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Stat4, a novel gamma interferon activation site-binding protein expressed in early myeloid differentiation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Isoform-specific amino-terminal domains dictate DNA-binding properties of ROR alpha, a novel family of orphan hormone nuclear receptors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Physical mapping of the minimal region of loss in 5q- chromosome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

The orphan nuclear receptor ROR alpha (RORA) maps to a conserved region of homology on human chromosome 15q21-q22 and mouse chromosome 9.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Use of the ‘Perceptron’ algorithm to distinguish translational initiation sites inE. coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Methods for calculating the probabilities of finding patterns in sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

The PML-RARα fusion mRNA generated by the t(15;17) translocation in acute promyelocytic leukemia encodes a functionally altered RAR

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Selection of high affinity RNA ligands to the bacteriophage R17 coat protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Identification of breakpoints in t(8;21) acute myelogenous leukemia and isolation of a fusion transcript, AML1/ETO, with similarity to Drosophila segmentation gene, runt

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

6 September 2017

Aberrant association of promyelocytic leukemia protein-retinoic acid receptor-alpha with coactivators contributes to its ability to regulate gene expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

14 September 2017

Vitamin D receptor signaling of monocytic differentiation in human leukemia cells: role of MAPK pathways in transcription factor activation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

14 September 2017

c-Myc rapidly induces acute myeloid leukemia in mice without evidence of lymphoma-associated antiapoptotic mutations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

14 September 2017

PML-RARA-RXR oligomers mediate retinoid and rexinoid/cAMP cross-talk in acute promyelocytic leukemia cell differentiation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

14 September 2017

Fos modulates myeloid cell survival and differentiation and partially abrogates the c-Myc block in terminal myeloid differentiation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

14 September 2017

AML1 is functionally regulated through p300-mediated acetylation on specific lysine residues.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

14 September 2017

Common mechanism for oncogenic activation of MLL by forkhead family proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

14 September 2017

Discrete roles of the Spc1 kinase and the Atf1 transcription factor in the UV response of Schizosaccharomyces pombe

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

14 September 2017

Computationally identifying novel NF-kappa B-regulated immune genes 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=2374711

27 September 2017

Isolation and characterization of a human STAT1 gene regulatory element. Inducibility by interferon (IFN) types I and II and role of IFN regulatory factor-1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

27 September 2017

Constitutive activation of STAT3 and STAT5 is induced by leukemic fusion proteins with protein tyrosine kinase activity and is sufficient for transformation of hematopoietic precursor cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

27 September 2017

Granulocyte-macrophage colony-stimulating factor induces the transcriptional activation of egr-1 through a protein kinase A-independent signaling pathway

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

27 September 2017

Commonly dysregulated genes in murine APL cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

23 June 2018

Leukemia initiated by PMLRARalpha: the PML domain plays a critical role while retinoic acid-mediated transactivation is dispensable

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

23 June 2018

The chimeric E2A-HLF transcription factor abrogates p53-induced apoptosis in myeloid leukemia cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

23 June 2018

GABP cooperates with c-Myb and C/EBP to activate the neutrophil elastase promoter

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

23 June 2018

PReMod: a database of genome-wide mammalian cis-regulatory module predictions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

31 August 2018

Multilineage transcriptional priming and determination of alternate hematopoietic cell fates.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

31 August 2018

Normal hematopoiesis after conditional targeting of RXRalpha in murine hematopoietic stem/progenitor cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

31 August 2018

Pro-proliferative function of the long isoform of PML-RARalpha involved in acute promyelocytic leukemia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

31 August 2018

Rexinoid-triggered differentiation and tumor-selective apoptosis of acute myeloid leukemia by protein kinase A-mediated desubordination of retinoid X receptor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

31 August 2018

Alterations of lymphoid enhancer factor-1 isoform expression in solid tumors and acute leukemias

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

31 August 2018

Smad7 alters cell fate decisions of human hematopoietic repopulating cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

31 August 2018

A Bayesian approach to reconstructing genetic regulatory networks with hidden factors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

31 August 2018

Computational discovery of gene modules and regulatory networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

31 August 2018

Distinct interactions of PML-RARalpha and PLZF-RARalpha with co-repressors determine differential responses to RA in APL.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

31 August 2018

Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

1 October 2018

The myeloid master regulator transcription factor PU.1 is inactivated by AML1-ETO in t(8;21) myeloid leukemia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2374711

3 December 2018

A-type lamins are essential for TGF-beta1 induced PP2A to dephosphorylate transcription factors

1 reference

https://pubmed.ncbi.nlm.nih.gov/18291030

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Distal enhancer elements transcribe intergenic RNA in the IL-10 family gene cluster

1 reference

https://pubmed.ncbi.nlm.nih.gov/18291030

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

RXR is an essential component of the oncogenic PML/RARA complex in vivo

1 reference

https://pubmed.ncbi.nlm.nih.gov/18291030

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Recruitment of RXR by Homotetrameric RARα Fusion Proteins Is Essential for Transformation

1 reference

https://pubmed.ncbi.nlm.nih.gov/18291030

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/GB-2008-9-2-R38

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

ResearchGate publication ID

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