(Q33507905)

27 July 2017

title

Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks (English)

1 reference

27 July 2017

Brian P Dalrymple

5

0 references

author name string

Nicholas J Hudson

1

1 reference

27 July 2017

Antonio Reverter

2

1 reference

27 July 2017

YongHong Wang

3

1 reference

27 July 2017

Paul L Greenwood

4

1 reference

27 July 2017

language of work or name

English

0 references

publication date

1 October 2009

1 reference

27 July 2017

1 reference

27 July 2017

volume

4

1 reference

27 July 2017

issue

10

1 reference

27 July 2017

page(s)

e7249

1 reference

Creative Commons Attribution 4.0 International

27 July 2017

copyright license

start time

1 October 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

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

cites work

Diversity and complexity in DNA recognition by transcription factors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

The genome sequence of taurine cattle: a window to ruminant biology and evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Inference of regulatory gene interactions from expression data using three-way mutual information

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Reverse-engineering transcriptional modules 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=2749936

A census of human transcription factors: function, expression and evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Learning a prior on regulatory potential from eQTL 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=2749936

Human gene coexpression landscape: confident network derived from tissue transcriptomic 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=2749936

Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Leptin inhibits rosiglitazone-induced adipogenesis in murine primary adipocytes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Control of muscle mitochondria by insulin entails activation of Akt2-mtNOS pathway: implications for the metabolic syndrome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

eQED: an efficient method for interpreting eQTL associations using protein networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Fast/Glycolytic muscle fiber growth reduces fat mass and improves metabolic parameters in obese 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=2749936

FoxM1 regulates growth factor-induced expression of kinase-interacting stathmin (KIS) to promote cell cycle progression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Weighted gene coexpression network analysis strategies applied to mouse weight

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Orphan nuclear receptor estrogen-related receptor alpha is essential for adaptive thermogenesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

A gene coexpression network for bovine skeletal muscle inferred from microarray 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=2749936

CDCA4 is an E2F transcription factor family-induced nuclear factor that regulates E2F-dependent transcriptional activation and cell proliferation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Redundant roles of Sox17 and Sox18 in postnatal angiogenesis 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=2749936

A general framework for weighted gene co-expression network 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=2749936

Microarray analysis of PDGFR alpha+ populations in ES cell differentiation culture identifies genes involved in differentiation of mesoderm and mesenchyme including ARID3b that is essential for development of embryonic mesenchymal 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=2749936

Global and gene-specific analyses show distinct roles for Myod and Myog at a common set of promoters

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

The next generation of literature analysis: integration of genomic analysis into text mining

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Characterization of E2F8, a novel E2F-like cell-cycle regulated repressor of E2F-activated transcription

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Constructing transcriptional regulatory networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Mitochondria, telomeres and cell senescence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

MatInspector and beyond: promoter analysis based on transcription 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=2749936

Reverse engineering of regulatory networks in human B 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=2749936

An initial blueprint for myogenic differentiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

CTIP1 and CTIP2 are differentially expressed during 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=2749936

Regulation of muscle fiber type and running endurance by PPARdelta

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Effect of a C/EBP gene replacement on mitochondrial biogenesis in fat 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=2749936

Angiopoietin-3 is tethered on the cell surface via heparan sulfate proteoglycans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Six1 and Eya1 expression can reprogram adult muscle from the slow-twitch phenotype into the fast-twitch phenotype

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Coexpression analysis of human genes across many microarray data sets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Quantitative genetic variation: a post-modern view

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Network biology: understanding the cell's functional organization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Interaction of human HSP22 (HSPB8) with other small heat shock proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

The highly conserved Ndc80 complex is required for kinetochore assembly, chromosome congression, and spindle checkpoint activity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate 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=2749936

Transcriptional co-activator PGC-1 alpha drives the formation of slow-twitch muscle fibres

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Mitochondrial transcription factors B1 and B2 activate transcription of human mtDNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Single cysteine to tyrosine transition inactivates the growth inhibitory function of Piedmontese myostatin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Formation of brainstem (nor)adrenergic centers and first-order relay visceral sensory neurons is dependent on homeodomain protein Rnx/Tlx3

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Effects of genetic background on thermoregulation and fatty acid-induced uncoupling of mitochondria in UCP1-deficient 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=2749936

Genetic network inference: from co-expression clustering to reverse engineering

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Induction of cell cycle entry and cell death in postmitotic lens fiber cells by overexpression of E2F1 or E2F2

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Human skeletal muscle fibres: molecular and functional diversity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Targeted disruption of Hoxd9 and Hoxd10 alters locomotor behavior, vertebral identity, and peripheral nervous system 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=2749936

Identification of a novel tropomodulin isoform, skeletal tropomodulin, that caps actin filament pointed ends in fast skeletal muscle.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Matrix-dependent Tiam1/Rac signaling in epithelial cells promotes either cell-cell adhesion or cell migration and is regulated by phosphatidylinositol 3-kinase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Inhibition of Stat1-mediated gene activation by PIAS1

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Regulation of skeletal muscle mass in mice by a new TGF-beta superfamily member

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Differential cell cycle effects induced by E2F1 mutants

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Structure and function of type II DNA topoisomerases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Embryonic expression of Lim-1, the mouse homolog of Xenopus Xlim-1, suggests a role in lateral mesoderm differentiation and neurogenesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Molecular mechanisms of the expression of cytosolic and mitochondrial isozyme 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=2749936

Evolution of energy metabolism. Proton permeability of the inner membrane of liver mitochondria is greater in a mammal than in a reptile

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Extracellular proteins that modulate cell-matrix interactions. SPARC, tenascin, and thrombospondin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Molecular characterization of a rat negative regulator with a basic helix-loop-helix structure predominantly expressed in the developing nervous system

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

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21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

An amphioxus homeobox gene: sequence conservation, spatial expression during development and insights into vertebrate evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

Evolvability and hierarchy in rewired bacterial gene networks

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Evolution of eukaryotic transcription circuits

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Gene co-expression network topology provides a framework for molecular characterization of cellular state

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Gene expression patterns during intramuscular fat development in cattle.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Discerning static and causal interactions in genome-wide reverse engineering problems.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Lessons from the DREAM2 Challenges

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Reverse engineering gene regulatory networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

The transcriptional activation function of the HIF-like factor requires phosphorylation at a conserved threonine

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

MusTRD can regulate postnatal fiber-specific expression.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Myosin light chain isoform expression among single mammalian skeletal muscle fibers: species variations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Autoregulatory control of E2F1 expression in response to positive and negative regulators of cell cycle progression

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Lsh is required for meiotic chromosome synapsis and retrotransposon silencing in female germ cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Cross-talk between MCP-3 and TGFbeta promotes fibroblast collagen biosynthesis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Expression of two novel mouse Iroquois homeobox genes during neurogenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Expression of murine Lhx5 suggests a role in specifying the forebrain

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0007249

Retinoids are produced by glia in the lateral ganglionic eminence and regulate striatal neuron differentiation.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2749936

SHC1, a high pH inducible gene required for growth at alkaline pH in Saccharomyces cerevisiae

31 October 2018

1 reference

12 December 2020

Metabolic adaptations to marathon training and racing

1 reference

12 December 2020

[Effect of Tiam1 overexpression on proliferation and metastatic potential of human colorectal cancer]

1 reference

12 December 2020

Gene expression profiling of bovine skeletal muscle in response to and during recovery from chronic and severe undernutrition

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0007249

Identifiers

DOI

1 reference

27 July 2017

0 references

1 reference

27 July 2017

1 reference