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Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation

Daniel M. Kemp, N. R. Nirmala, Joseph D. Szustakowski
2007 Computer applications in the biosciences : CABIOS  
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

Mathilde Janot, Aymeric Audfray, Céline Loriol, Agnès Germot, Abderrahman Maftah, Fabrice Dupuy
2009 BMC Genomics  
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

A.H.V. Remels, H.R. Gosker, R.C. Langen, M. Polkey, P. Sliwinski, J. Galdiz, B. van den Borst, N.A. Pansters, A.M.W.J. Schols
2014 Biochimica et Biophysica Acta - Molecular Basis of Disease  
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 ( 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

Shuo Yang, Allison Weske, Yingqiu Du, Juliana M. Valera, Aaron N. Johnson
2020 Development  
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

Christopher J. Walsh, Jane Batt, Margaret S. Herridge, Sunita Mathur, Gary D. Bader, Pingzhao Hu, Claudia C. dos Santos
2016 Scientific Reports  
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  
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]

Shuo Yang, Allison Weske, Yingqiu Du, Juliana M Valera, Aaron Johnson
2019 bioRxiv   pre-print
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

Ida Chow
2004 Developmental Biology  
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]

Jiekun Yang, Maria Vamvini, Pasquale Nigro, Li-Lun Ho, Kiki Galani, Marcus Alvarez, Yosuke Tanigawa, Markku Laakso, Leandro Agudelo, Paivi Pajukanta, Roeland Middelbeek, Kevin Grove (+2 others)
2021 bioRxiv   pre-print
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

David Karasik, Douglas P. Kiel
2010 Bone  
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

Margaret Stromecki, Nazanin Tatari, Ludivine Coudière Morrison, Ravinder Kaur, Jamie Zagozewski, Gareth Palidwor, Vijay Ramaswamy, Patryk Skowron, Matthias Wölfl, Till Milde, Marc R. Del Bigio, Michael D. Taylor (+1 others)
2018 Molecular Oncology  
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

Xinyang Hu, Rongrong Wu, Lina A Shehadeh, Qing Zhou, Cizhong Jiang, Xin Huang, Ling Zhang, Feng Gao, Xianbao Liu, Hong Yu, Keith A Webster, Jian'an Wang
2014 BMC Genomics  
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

Gele Liu, Brian T. David, Matthew Trawczynski, Richard G. Fessler
2019 Stem Cell Reviews and Reports  
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  
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]

Peng He, Brian A Williams, Diane Trout, Georgi K Marinov, Henry Amrhein, Libera Berghella, Say-Tar Goh, Ingrid Plajzer-Frick, Veena Afzal, Len A Pennacchio, Diane E Dickel, Axel Visel (+4 others)
2020 bioRxiv   pre-print
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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