scholarly journals A Novel Approach for Pathway Analysis of GWAS Data Highlights Role of BMP Signaling and Muscle Cell Differentiation in Colorectal Cancer Susceptibility

2017 ◽  
Vol 20 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Aniket Mishra ◽  
Stuart MacGregor
Keyword(s):  
Colorectal Cancer ◽  
Cell Differentiation ◽  
Muscle Cell ◽  
Complex Traits ◽  
Meta Analysis ◽  
Bmp Signaling ◽  
Genome Wide Association Studies ◽  
Muscle Cell Differentiation ◽  
Gene Sets ◽  
Wide Range

Genome-wide association studies (GWAS) have revolutionized the field of gene mapping. As the GWAS field matures, it is becoming clear that for many complex traits, a proportion of the missing heritability is attributable to common variants of individually small effect. Detecting these small effects individually can be difficult, and statistical power would be increased if relevant variants could be grouped together for testing. Here, we propose a VEGAS2Pathway approach that aggregates association strength of individual markers into pre-specified biological pathways. It accounts for gene size and linkage disequilibrium between markers using simulations from the multivariate normal distribution. Pathway size is taken into account via a resampling approach. Importantly, since the approach only requires summary data, the method can easily be applied in all GWASs, including meta-analysis, singleton-based, family-based, and DNA-pooling-based designs. This approach is implemented in a user-friendly web page https://vegas2.qimrberghofer.edu.au and a command line tool. The web implementation uses gene-sets from the gene ontology (GO), curated gene-sets from MSigDB (containing canonical pathways and gene-sets from BIOCARTA, REACTOME, KEGG databases), PANTHER, and pathway commons databases, enabling analysis of a wide range of complex traits. We applied this method on a colorectal cancer GWAS meta-analysis data set (10,934 cases, 12,328 controls) from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). We report statistically significant enrichment of association signal for the ‘BMP signaling’ and ‘muscle cell differentiation’ pathways, suggesting a possible role for these pathways onto the risk of colorectal cancer.

scholarly journals A Novel Approach for Pathway Analysis of GWAS Data Highlights Role of BMP Signaling and Muscle Cell Differentiation in Colorectal Cancer Susceptibility – Erratum

2017 ◽  
Vol 20 (2) ◽  
pp. 186-186 ◽  
Author(s):  
Aniket Mishra ◽  
Stuart MacGregor
Keyword(s):  
Colorectal Cancer ◽  
Cell Differentiation ◽  
Medical Research ◽  
Pathway Analysis ◽  
Cancer Susceptibility ◽  
Bmp Signaling ◽  
Cancer Family ◽  
Muscle Cell Differentiation ◽  
Novel Approach

The publishers regret to announce that the affiliation for the above paper was incorrectly inserted. The correct affiliation is below:Aniket Mishra1, Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and the Colorectal Cancer Family Registry (CCFR), and Stuart MacGregor11 Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia

scholarly journals C6ORF32 is upregulated during muscle cell differentiation and induces the formation of cellular filopodia

2007 ◽  
Vol 301 (1) ◽  
pp. 70-81 ◽  
Author(s):  
Soonsang Yoon ◽  
Michael J. Molloy ◽  
Melissa P. Wu ◽  
Douglas B. Cowan ◽  
Emanuela Gussoni
Keyword(s):  
Cell Differentiation ◽  
Muscle Cell ◽  
Muscle Cell Differentiation

Increased Mitochondrial Biogenesis and Function Is Necessary for Muscle Cell Differentiation

2015 ◽  
Vol 87 ◽  
pp. S131
Author(s):  
Neelu E Varghese ◽  
Gobinath Shanmugam ◽  
Daniel J Bolus ◽  
Balu K Chacko ◽  
Victor M Darley-Usmar ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Muscle Cell ◽  
Mitochondrial Biogenesis ◽  
Muscle Cell Differentiation ◽  
And Function

scholarly journals Posttranscriptional control of embryonic rat skeletal muscle protein synthesis. Control at the level of translation by endogenous RNA.

1988 ◽  
Vol 107 (3) ◽  
pp. 1085-1098 ◽  
Author(s):  
C R Vanderburg ◽  
M A Nathanson
Keyword(s):  
Skeletal Muscle ◽  
Cell Differentiation ◽  
Muscle Cell ◽  
Translational Control ◽  
Muscle Protein ◽  
Muscle Protein Synthesis ◽  
Skeletal Muscle Protein ◽  
Rat Skeletal Muscle ◽  
Total Rna ◽  
Muscle Cell Differentiation

The onset of muscle cell differentiation is associated with increased transcription of muscle-specific mRNA. Studies from this laboratory using 19-d embryonic rat skeletal muscle, suggest that additional, posttranscriptional controls regulate maturation of muscle tissue via a quantitative effect upon translation, and that the regulatory component may reside within the poly A- RNA pool (Nathanson, M.A., E.W. Bush, and C. Vanderburg. 1986. J. Biol. Chem. 261:1477-1486). To further characterize muscle cell translational control, embryonic and adult total RNA were separated into oligo(dT)cellulose-bound (poly A+) and -unbound (poly A-) pools. Unbound material was subjected to agarose gel electrophoresis to resolve constituents of varying molecular size and mechanically cut into five fractions. Material of each fraction was electroeluted and recovered by precipitation. Equivalent loads of total RNA from 19-20-d embryonic rat skeletal muscle exhibited a 40% translational inhibition in comparison to its adult counterpart. Inhibition was not due to decreased message abundance because embryonic, as well as adult muscle, contained equivalent proportions of poly A+ mRNA. An inhibition assay, based upon the translatability of adult RNA and its inhibition by embryonic poly A- RNA, confirmed that inhibition was associated with a 160-2,000-nt poly A- fraction. Studies on the chemical composition of this fraction confirmed its RNA composition, the absence of ribonucleoprotein, and that its activity was absent from similarly fractionated adult RNA. Rescue of inhibition could be accomplished by addition of extra lysate or mRNA; however, smaller proportions of lysate were required, suggesting a strong interaction of inhibitor and components of the translational apparatus. Additional studies demonstrated that the inhibitor acted at the level of initiation, in a dose-dependent fashion. The present studies confirm the existence of translational control in skeletal muscle and suggest that it operates at the embryonic to adult transition. A model of muscle cell differentiation, based upon transcriptional control at the myoblast level, followed by translational regulation at the level of the postmitotic myoblast and/or myotube, is proposed.

Set7 regulates smooth muscle cell differentiation

2017 ◽  
Vol 263 ◽  
pp. e20
Author(s):  
Natasha Kelly Tuano ◽  
Jun Okabe ◽  
Mark Ziemann ◽  
Mark E. Cooper ◽  
Assam El-Osta
Keyword(s):  
Smooth Muscle ◽  
Cell Differentiation ◽  
Smooth Muscle Cell ◽  
Muscle Cell ◽  
Muscle Cell Differentiation ◽  
Smooth Muscle Cell Differentiation
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