Year : 2020 | Volume
: 11 | Issue : 3 | Page : 198--203
Muscle biopsies differ in relation to expression of fiber-type specific genes
Rakesh Kumar1, Krishna Kumar Ojha1, Pooja Kushwaha2, Vijay Kumar Singh1
1 Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar, India
2 Department of Statistics, Central University of South Bihar, Gaya, Bihar, India
Background: Skeletal muscle transcriptome has been analyzed to report muscle-specific biomarkers, but muscle heterogeneity has largely been overlooked in pursuit of formulating a balanced design. Given the heterogeneity of muscle tissue in terms of both function and fiber-type composition, there could be several unaccounted sources of variation affecting the gene expression profile of skeletal muscles. Categorization of muscle transcriptome according to the source of variation will not only improve the power of transcriptome comparison tests but also will help to identify unaccounted biological sources of variation. Materials and Methods: Gene expression profile of normal skeletal muscle subjects (GSE18732) were analyzed with R-statistical software and Bioconductor packages. Gene-sets were prepared by grouping Affymetrix probes according to biological processes they were annotated. Coherence score and associated P values were calculated for each gene-set. All gene-sets having P < 0.05 were selected as coherent gene-set. Results: We have analyzed gene-sets and used coherence scores to measure the degree of coregulation between genes of a gene-set. We have shown that coherent gene-sets have a better chance to classify samples into biologically relevant subgroups as compared to noncoherent gene-sets. Further, we have applied the developed method to the muscle gene expression profiles and found that muscle fiber-type proportion in collected biopsies is one of the most prominent unaccounted “source of variations” affecting gene expression measurements. Conclusion: The sample classification produced based on the expression profile of genes belonging to coherent gene-sets has a better chance to result in biologically meaningful clusters.
Dr. Vijay Kumar Singh
Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Village – Karhara, Post. Fatehpur, Gaya, Bihar.
|How to cite this article:|
Kumar R, Ojha KK, Kushwaha P, Singh VK. Muscle biopsies differ in relation to expression of fiber-type specific genes.J Diabetol 2020;11:198-203
|How to cite this URL:|
Kumar R, Ojha KK, Kushwaha P, Singh VK. Muscle biopsies differ in relation to expression of fiber-type specific genes. J Diabetol [serial online] 2020 [cited 2020 Oct 20 ];11:198-203
Available from: https://www.journalofdiabetology.org/article.asp?issn=2078-7685;year=2020;volume=11;issue=3;spage=198;epage=203;aulast=Kumar;type=0