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Analysis of differential gene expression and novel transcript units of ovine muscle transcriptomes.

Zhang C, Wang G, Wang J, Ji Z, Dong F, Chao T - PLoS ONE (2014)

Bottom Line: Among the 123,678 novel predicted transcript units (TUs), 15,015 units were predicted protein sequences.The reliability of the sequencing data was verified through qRT-PCR analysis of 12 genes.These results will provide useful information for functional genetic research in the future.

View Article: PubMed Central - PubMed

Affiliation: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China ; College of Biological and Agricultural Engineering, Weifang University, Key Laboratory of Biochemistry and Molecular Biology in Universities of Shandong, Weifang, China.

ABSTRACT
In this study, we characterized differentially expressed genes (DEGs) between the muscle transcriptomes of Small-tailed Han sheep and Dorper sheep and predicted novel transcript units using high-throughput RNA sequencing technology. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that 1,300 DEGs were involved in cellular processes, metabolic pathways, and the actin cytoskeleton pathway. Importantly, we identified 34 DEGs related to muscle cell development and differentiation. Additionally, we were able to optimize the gene structure and predict the untranslated regions (UTRs) for some of the DEGs. Among the 123,678 novel predicted transcript units (TUs), 15,015 units were predicted protein sequences. The reliability of the sequencing data was verified through qRT-PCR analysis of 12 genes. These results will provide useful information for functional genetic research in the future.

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Gene ontology classification for the DEGs.The figure shows the GO enrichment of the differentially expressed genes in terms of molecular function, cellular components, and biological processes.
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pone-0089817-g001: Gene ontology classification for the DEGs.The figure shows the GO enrichment of the differentially expressed genes in terms of molecular function, cellular components, and biological processes.

Mentions: To further investigate the biological importance of the differentially expressed genes, we determined the functional categories of each gene by querying the GO database (http://www.geneontology.org/GO.database.shtml). The 1,300 DEGs were categorized into 56 functional groups based on sequence homology, which included 24 biological process, 15 cellular component, and 17 molecular function annotation. Among these functional groups, there was annotation of 82.00% (1,066/1,300), 87.46% (1,137/1,300), and 82.08% (1,067/1,300) of the DEGs, respectively (Figure 1).


Analysis of differential gene expression and novel transcript units of ovine muscle transcriptomes.

Zhang C, Wang G, Wang J, Ji Z, Dong F, Chao T - PLoS ONE (2014)

Gene ontology classification for the DEGs.The figure shows the GO enrichment of the differentially expressed genes in terms of molecular function, cellular components, and biological processes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3935930&req=5

pone-0089817-g001: Gene ontology classification for the DEGs.The figure shows the GO enrichment of the differentially expressed genes in terms of molecular function, cellular components, and biological processes.
Mentions: To further investigate the biological importance of the differentially expressed genes, we determined the functional categories of each gene by querying the GO database (http://www.geneontology.org/GO.database.shtml). The 1,300 DEGs were categorized into 56 functional groups based on sequence homology, which included 24 biological process, 15 cellular component, and 17 molecular function annotation. Among these functional groups, there was annotation of 82.00% (1,066/1,300), 87.46% (1,137/1,300), and 82.08% (1,067/1,300) of the DEGs, respectively (Figure 1).

Bottom Line: Among the 123,678 novel predicted transcript units (TUs), 15,015 units were predicted protein sequences.The reliability of the sequencing data was verified through qRT-PCR analysis of 12 genes.These results will provide useful information for functional genetic research in the future.

View Article: PubMed Central - PubMed

Affiliation: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China ; College of Biological and Agricultural Engineering, Weifang University, Key Laboratory of Biochemistry and Molecular Biology in Universities of Shandong, Weifang, China.

ABSTRACT
In this study, we characterized differentially expressed genes (DEGs) between the muscle transcriptomes of Small-tailed Han sheep and Dorper sheep and predicted novel transcript units using high-throughput RNA sequencing technology. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that 1,300 DEGs were involved in cellular processes, metabolic pathways, and the actin cytoskeleton pathway. Importantly, we identified 34 DEGs related to muscle cell development and differentiation. Additionally, we were able to optimize the gene structure and predict the untranslated regions (UTRs) for some of the DEGs. Among the 123,678 novel predicted transcript units (TUs), 15,015 units were predicted protein sequences. The reliability of the sequencing data was verified through qRT-PCR analysis of 12 genes. These results will provide useful information for functional genetic research in the future.

Show MeSH