Differentially Expressed Genes and Related Pathways in the Ovine Muscle Transcriptome pre and postnatal Using the Integration of Microarray and RNA-seq Data

Document Type : Research Articles

Authors

• Fahime Mohammadi ¹
• Mojtaba Tahmoorespour ¹
• Ali Javadmanesh ^{1, 2}

¹ Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran

² Industrial Biotechnology Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran

https://doi.org/10.22067/jcmr.2024.86067.1085

Abstract

The formation of muscle myofibrils as well as the growth and hypertrophy of the muscle are controlled by various genes. Bioinformatics tools could also be used to integrate and analyze heterogeneous data sets. In this study, the DEGs, gene network, GO and biological pathways have been investigated by incorporating the data obtained by expression array and RNA-Seq, related to the muscle tissue transcriptome of Texel sheep respectively before and after birth. The microarray expression profile was extracted from the GEO database, and the RNA-Seq expression profile was extracted from the ArrayExpress database. DEGs were identified with limma and sva software packages in R environment and a gene network was drawn with STRING, an application in Cytoscape software. The clustering and gene ontology were done with CytoCluster and ClueGO applications. The results showed a significant difference between the juvenile and 70-day embryonic stages the expression of 103 genes, between the adult and juvenile stages the expression of 28 genes and between the adult and 70-day embryonic stages the expression of 62 genes. By constructing the gene network between these DEGs, a total of 37 selected genes were identified. The results revealed the function of these genes in cell proliferation, protein synthesis, formation and organization of myofibrils, muscle contraction, and lipid metabolism. By integrating the expression data, this study provided a general view of the differences in transcriptomes in the muscle tissue of sheep. Also, the selected genes such as BUB1, RFC2, KIAA0101, RAD51, CKS2, and UQCRB were identified for the first time being reported as effective genes for myogenesis.

Keywords

• DEGs
• Gen Ontology
• Physiological pathway
• Muscle tissue
• Sheep

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