Screening and Identification of Muscle-Specific Candidate Genes via Mouse Microarray Data Analysis

Sayed Haidar Abbas Raza; Chengcheng Liang; Wang Guohua; Sameer D Pant; Zuhair M Mohammedsaleh; Abdullah F Shater; Mashael Alhumaidi Alotaibi; Rajwali Khan; Nicola Schreurs; Gong Cheng; Chugang Mei; Linsen Zan

doi:10.3389/fvets.2021.794628

Screening and Identification of Muscle-Specific Candidate Genes via Mouse Microarray Data Analysis

Front Vet Sci. 2021 Dec 13:8:794628. doi: 10.3389/fvets.2021.794628. eCollection 2021.

Authors

Affiliations

¹ College of Animal Science and Technology, Northwest A&F University, Yangling, China.
² School of Animal & Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia.
³ Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia.
⁴ Department of Biology, College of Science, Jouf University, Sakaka, Saudi Arabia.
⁵ Department of Livestock Management, Breeding and Genetic, The University of Agriculture Peshawar, Peshawar, Pakistan.
⁶ Animal Science, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand.
⁷ National Beef Cattle Improvement Center, Northwest A&F University, Yangling, China.

Abstract

Muscle tissue is involved with every stage of life activities and has roles in biological processes. For example, the blood circulation system needs the heart muscle to transport blood to all parts, and the movement cannot be separated from the participation of skeletal muscle. However, the process of muscle development and the regulatory mechanisms of muscle development are not clear at present. In this study, we used bioinformatics techniques to identify differentially expressed genes specifically expressed in multiple muscle tissues of mice as potential candidate genes for studying the regulatory mechanisms of muscle development. Mouse tissue microarray data from 18 tissue samples was selected from the GEO database for analysis. Muscle tissue as the treatment group, and the other 17 tissues as the control group. Genes expressed in the muscle tissue were different to those in the other 17 tissues and identified 272 differential genes with highly specific expression in muscle tissue, including 260 up-regulated genes and 12 down regulated genes. is the genes were associated with the myofibril, contractile fibers, and sarcomere, cytoskeletal protein binding, and actin binding. KEGG pathway analysis showed that the differentially expressed genes in muscle tissue were mainly concentrated in pathways for AMPK signaling, cGMP PKG signaling calcium signaling, glycolysis, and, arginine and proline metabolism. A PPI protein interaction network was constructed for the selected differential genes, and the MCODE module used for modular analysis. Five modules with Score > 3.0 are selected. Then the Cytoscape software was used to analyze the tissue specificity of differential genes, and the genes with high degree scores collected, and some common genes selected for quantitative PCR verification. The conclusion is that we have screened the differentially expressed gene set specific to mouse muscle to provide potential candidate genes for the study of the important mechanisms of muscle development.

Keywords: bioinformatics; biotechnology; differential genes; microarray analysis; muscle development.