Exploring the Molecular Mechanism of Skeletal Muscle Development in Ningxiang Pig by Weighted Gene Co-Expression Network Analysis
Abstract
:1. Introduction
2. Results
2.1. Module Identification
2.2. Screening Skeletal Muscle Development-Related Co-Expression Gene Modules by WGCNA
2.2.1. Development Stage Feature Module and Hub Gene Identification
2.2.2. Key Modules of Muscle Fiber-Related Indexes of LD and Identification of Hub Gene
2.2.3. Key Module of Amino Acids and Fatty Acids in LD and Identification of Hub Gene
2.3. Functional Enrichment Analysis of Characteristic Genes of Muscle Phenotype Related Modules
2.3.1. Functional Enrichment Analysis of Hub Genes of Related Modules in Muscle Development Stage
2.3.2. Functional Enrichment Analysis of Characteristic Genes of Muscle Fiber-Related Modules
2.3.3. Enrichment Analysis of Characteristic Genes of Fatty Acid-Related Modules in LD
2.3.4. Overlapping Analysis of Characteristic Genes and Hub Genes of Muscle Phenotype
2.4. Protein–Protein Interaction (PPI) and Transcription Factor (TF) Analysis of Muscle Phenotype-Related Genes
3. Discussion
4. Materials and Methods
4.1. Experimental Animals and Sample Preparation
4.2. Phenotypic Detection
4.2.1. Detection of Type Proportion, Diameter and Density of Muscle Fibers
4.2.2. Detection of Fatty Acids and Amino Acids
4.3. RNA-Seq
4.4. Bioinformatics Analysis
4.4.1. Sequencing Data Sorting and Trimming
4.4.2. WGCNA Analysis
4.4.3. Enrichment Analysis of GO and KEGG
4.4.4. Prediction and Analysis of Transcription Factors
4.4.5. Protein–Protein Interaction Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Yu, Z.; Ai, N.; Xu, X.; Zhang, P.; Jin, Z.; Li, X.; Ma, H. Exploring the Molecular Mechanism of Skeletal Muscle Development in Ningxiang Pig by Weighted Gene Co-Expression Network Analysis. Int. J. Mol. Sci. 2024, 25, 9089. https://doi.org/10.3390/ijms25169089
Yu Z, Ai N, Xu X, Zhang P, Jin Z, Li X, Ma H. Exploring the Molecular Mechanism of Skeletal Muscle Development in Ningxiang Pig by Weighted Gene Co-Expression Network Analysis. International Journal of Molecular Sciences. 2024; 25(16):9089. https://doi.org/10.3390/ijms25169089
Chicago/Turabian StyleYu, Zonggang, Nini Ai, Xueli Xu, Peiwen Zhang, Zhao Jin, Xintong Li, and Haiming Ma. 2024. "Exploring the Molecular Mechanism of Skeletal Muscle Development in Ningxiang Pig by Weighted Gene Co-Expression Network Analysis" International Journal of Molecular Sciences 25, no. 16: 9089. https://doi.org/10.3390/ijms25169089