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Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation
2007
Computer applications in the biosciences : CABIOS
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Comparisons of the transcriptional state of myoblasts and differentiated myotubes via a robust variance test implicated several novel pathways in muscle cell differentiation previously overlooked by a ...
Motivation: We describe an extension of the pathway-based enrichment approach for analyzing microarray data via a robust test for transcriptional variance. ...
ACKNOWLEDGEMENTS The authors thank Penelope Kosinski for discussions motivating the application of a variance test; Leah Martell and Mathis Thoma for advice on statistical tests; Qicheng Ma for general ...
doi:10.1093/bioinformatics/btm116
pmid:17392327
fatcat:ehbl5245crhlpg3m25unu5ivsu
Glycogenome expression dynamics during mouse C2C12 myoblast differentiation suggests a sequential reorganization of membrane glycoconjugates
2009
BMC Genomics
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Conclusion: For the first time, these results provide a broad description of the expression dynamics of glycogenes during C2C12 differentiation. ...
In particular, an increase in the quantity of ganglioside G M3 at the cell surface of myoblasts is suggestive of its potential role during the initial steps of myogenic differentiation. ...
Acknowledgements This work was supported by the Limousin Regional Council, and the French Ministry of Research and Technology doctoral fellowships of M. Janot and A. Audfray. ...
doi:10.1186/1471-2164-10-483
pmid:19843320
pmcid:PMC2772862
fatcat:un7xw6ndozfr3lwifzobbkysva
Classical NF-κB activation impairs skeletal muscle oxidative phenotype by reducing IKK-α expression
2014
Biochimica et Biophysica Acta - Molecular Basis of Disease
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The funding agency had no role in study design, in the collection, analysis and interpretation of data, in the writing of the report and in the decision to submit the article for publication. ...
This paper was written according to Uniform Requirements for manuscripts submitted to Biomedical journals (http://www.icmje.org).
Appendix A. ...
As the expression of both Pgc-1α and Pgc-1β are induced during myogenic differentiation [17, 22] , the observed effects of Ikk-α modulation on expression of the Pgc-1 molecules in the latter approach ...
doi:10.1016/j.bbadis.2013.11.001
pmid:24215713
fatcat:2auhflcezfculewehd7a4xv3fa
FGF signaling directs myotube guidance by regulating Rac activity
2020
Development
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Nascent myotubes undergo a dramatic morphological transformation during myogenesis, in which the myotubes elongate over several cell diameters and are directed to the correct muscle attachment sites. ...
Using transcriptomics, we found that components of the Fibroblast Growth Factor (FGF) signaling pathway were enriched in nascent myotubes in Drosophila embryos. ...
We are also grateful to the reviewers for the insights and suggestions that improved our manuscript. ...
doi:10.1242/dev.183624
pmid:31932350
pmcid:PMC7033734
fatcat:qrbhiez7mbcklfwd7gqgnuxtuy
Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness
2016
Scientific Reports
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Unsupervised co-expression network analysis of transcriptomic profiles identified discrete modules of co-expressed genes associated with the degree of muscle weakness and atrophy in early and sustained ...
A fundamental question regarding the pathomechanism of ICUAW is whether convergent transcriptional changes in response to muscle injury are associated with impaired recovery of muscle mass and strength ...
MEF2A has been shown to be upregulated during muscle regeneration 15 and is required for adult early myogenic (myoblast) differentiation and regeneration in response to injury 16 . ...
doi:10.1038/srep29334
pmid:27411715
pmcid:PMC4944143
fatcat:mv3mmhhf6ngudhz2v6dt23erx4
Society for Development Biology 64th Annual Meeting
2005
Developmental Biology
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In order to elucidate how Tbx transcription factors interact with other proteins within a regulatory network, we have identified a novel PDZ-LIM domain scaffolding protein, Lmp4, that specifically binds ...
Additional studies showed that the RNAi-like mechanism by which IESs are identified for elimination involves methylation of K9 on histone H3 and has other features of a highly conserved pathway for gene ...
Novel
Analysis of the
Differential Control of Death and Differentiation in Myoblasts
Lipid Rafts
Interaction Between Epithelium and Myogenic Progenitor Cells is Required for Tongue Morphogenesis ...
doi:10.1016/j.ydbio.2005.04.040
fatcat:jj63lzrujnfx7pt3uxl57spp4i
FGF signals direct myotube guidance by regulating Rho/Rac activity
[article]
2019
bioRxiv
pre-print
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Nascent myotubes undergo a dramatic morphological transformation during myogenesis in which the myotubes elongate over several cell diameters and choose the correct muscle attachment sites. ...
Using transcriptomics, we found that components of the Fibroblast Growth Factor (FGF) signaling pathway were enriched in nascent myotubes in Drosophila embryos. ...
Our study has identified a novel function for the FGF pathway during myogenesis, and has established a unique experimental framework to further investigate the discrete molecular mechanisms by which FGF ...
doi:10.1101/697789
fatcat:nhw4tnzlt5hqtnfnh2j3z2yuva
Abstracts: Society for Developmental Biology 63rd Annual Meeting
2004
Developmental Biology
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In vivo imaging of multiple labels should offer the ability to test the proposed mechanisms by following different GFP color variants on multiple molecular species in the same cell. ...
It has become possible to increase the resolution of MRI from the 1-mm voxels of a clinical instrument to approximately 10 Am. 2. ...
The Ret mutant mouse provides an ideal tool for identifying novel genes implicated in the development of the ENS. ...
doi:10.1016/j.ydbio.2004.05.002
fatcat:qhmbtrcvqnep5dm5lmrtgpsbqa
Single-cell dissection of obesity-exercise axis in adipose-muscle tissues
[article]
2021
bioRxiv
pre-print
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discovering and validating a novel CD140+/CD34+/SCA1- FAP population. ...
These changes reflected thermogenesis-vs-lipogenesis and hyperplasia-vs-hypertrophy shifts, clustered in pathways including extracellular matrix remodeling and circadian rhythm, and implicated complex ...
We thank Carlos Castorena and Angie Bookout for discussions and feedback on the high-fat diet and exercise training-regulated genes. We thank Karen Mohlke for analysis advice on the METSIM cohort. ...
doi:10.1101/2021.11.22.469622
fatcat:y6uyehmstzg3nptxhjszfztpiq
Evidence for pleiotropic factors in genetics of the musculoskeletal system
2010
Bone
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Understanding the crosstalk between muscles and bones will translate into a conceptual framework aimed at studying the pleiotropic genetic relationships in the etiology of complex musculoskeletal disease ...
We provide insights into several pathways and single genes, which apparently have a biologically plausible pleiotropic effect on both bones and muscles; the list is continuing to grow. ...
Notable, the mRNA level of IGFBP5, which modulates the activity of IGF-1, is decreased in skeletal muscle during fasting [193] . ...
doi:10.1016/j.bone.2010.01.382
pmid:20149904
pmcid:PMC4852133
fatcat:w47y3qshkzgbxjiqncevsjlily
Characterization of a novel OTX2-driven stem cell program in Group 3 and Group 4 medulloblastoma
2018
Molecular Oncology
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All analyses were checked for homogeneity of variances using a Brown-Forsythe test. Tumor data were analyzed using an independent sample one-tailed t test with Welch's correction. ...
an informed framework to pursue novel targeted therapies aimed at targeting the axon guidance genes pathways that facilitate differentiation of MB tumors cells. ...
Transcripts differentially expressed at least 2.0-fold (up-or downregulated) and with a value of P<0.05 were considered significant. ...
doi:10.1002/1878-0261.12177
pmid:29377567
pmcid:PMC5891039
fatcat:y435ufmu3fg55bggd6c5dyibi4
Severe hypoxia exerts parallel and cell-specific regulation of gene expression and alternative splicing in human mesenchymal stem cells
2014
BMC Genomics
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Exon analyses revealed 60 hypoxia-regulated AS events with splice indices (SI) >1.0 from 53 genes and a correlation between high SI and degree of transcript regulation. ...
Only 3 genes were differentially responsive to hypoxia at the gene (>2.0) and AS levels in both cell types. ...
The selective decrease of multiple myogenic gene markers by severe hypoxia is a novel observation of this study. ...
doi:10.1186/1471-2164-15-303
pmid:24758227
pmcid:PMC4234502
fatcat:nnuq3ecrrfdf5bljmws6ccua5u
Advances in Pluripotent Stem Cells: History, Mechanisms, Technologies, and Applications
2019
Stem Cell Reviews and Reports
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with a discussion of three-dimensional (3D) cell technology and future stem cell applications. ...
We begin by discussing experimental advances in the generation and differentiation of pluripotent stem cells (PSCs), next moving to the maintenance of stem cells in different culture types, and finishing ...
Acknowledgements The authors would like to thank Rush University Medical Center and the Rush Department of Neurosurgery for providing the funding for this study. ...
doi:10.1007/s12015-019-09935-x
pmid:31760627
pmcid:PMC6987053
fatcat:wmps2gnk4nddjf5oar5645efiu
Abstracts of the 6th Cachexia Conference, Milan, Italy, December 8-10, 2011
2011
Journal of Cachexia, Sarcopenia and Muscle
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For the two individuals with two biopsies each at different times, the differences in estimates of FSR were 14.3% and 20%. ...
We aimed to develop a novel method to determine skeletal muscle protein FSR to estimate habitual FSR in healthy individuals, over timescales comparable with clinical interventions, avoiding intravenous ...
Notch signaling.
1-11 Oleic acid accelerates myogenic differentiation through modulation of Notch and alpha-catenin pathways in muscle stem cells Carlos Hermano J. ...
doi:10.1007/s13539-011-0045-3
pmid:22476871
pmcid:PMC3222823
fatcat:yjup7zdkwvhcjd6h455t77av4a
The changing mouse embryo transcriptome at whole tissue and single-cell resolution
[article]
2020
bioRxiv
pre-print
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Focusing on the developing limb, scRNA-seq identified 25 known and candidate novel cell types, including progenitor and differentiating states with computationally inferred lineage relationships. ...
Integrating promoter sequence motifs with companion ENCODE epigenomic profiles identified a promoter de-repression mechanism unique to neuronal expression clusters and attributable to known and novel repressors ...
YZ; Bing Ren for leadership of the ENCODE mouse working group, Sarah A Teichmann, Lior Pachter, Cole Trapnell and Matt Thomson for discussions, and Hongbo Zhang and Krzysztof Polaski for discussion and ...
doi:10.1101/2020.06.14.150599
fatcat:2b7uao7ahbcdrp3i4hr7zmdhwm
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