Chinese Journal of Tissue Engineering Research ›› 2019, Vol. 23 ›› Issue (27): 4269-4274.doi: 10.3969/j.issn.2095-4344.1371
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Huang Hui, Wang Guangji
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the Natural Science Foundation of Hainan Province, No. 310122 (to WGJ)
Abstract:
BACKGROUND: Muscle atrophy is often associated with spinal cord injury, but its underlying mechanisms are still unclear. OBJECTIVE: To explore the molecular biological mechanism of muscle atrophy after spinal cord injury. METHODS: Gene profile GSE45550 for muscle atrophy after spinal cord injury in the gene expression database was analyzed. The gene expression profile GSE45550 included a control group (pre-spinal cord injury), an experimental group 1 (3 days after spinal cord injury), an experimental group 2 (8 days after spinal cord injury), and an experimental group 3 (14 days after spinal cord injury). The tissue was the soleus muscle of Sprague-Dawley rats (n=6/group). Four groups of sample data were then subjected to differential gene analysis, GO analysis, and pathway analysis. RESULTS AND CONCLUSION: Totally 2 513 differentially expressed genes were identified, of which Wnt16 Obfc1, Ufd1l, LOC100361067, Hhatl, Fxyd1, Psmc4, Tasp1, Mettl21c, and Ufd1l differential expressions were most significant. Biological processes such as biological process, G-protein coupled receptor signaling pathway, response to drug, transcription DNA-dependent, positive regulation of transcription DNA-dependent, oxidation-reduction process, ubiquitin-dependent protein catabolic process, apoptotic process, positive regulation of transcription from RNA polymeras, and fatty acid beta-oxidation, signaling pathways such as MAPK signaling, apoptosis, and citric acid cycle may play important roles. This study completely reveals the differentially expressed genes of muscle atrophy after spinal cord injury gene profiles, the involved biological processes, and signaling pathways. Wnt16 may be a key gene in muscle atrophy after spinal cord injury, providing molecular targets for future therapeutic progress.
Key words: spinal cord injury, muscle atrophy, pathway, gene, biological process, differential gene analysis, GO analysis, pathway analysis
CLC Number:
中图分类号:R459.9
R318
Huang Hui, Wang Guangji . Bioinformatics analysis of gene spectrum of muscle atrophy after spinal cord injury [J]. Chinese Journal of Tissue Engineering Research, 2019, 23(27): 4269-4274.
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URL: https://www.cjter.com/EN/10.3969/j.issn.2095-4344.1371
https://www.cjter.com/EN/Y2019/V23/I27/4269
2.1 差异基因分析结果 数据预处理后,总共有2 513个基因被确定为差异表达基因。这些差异基因为多分组间差异基因,结果显示在聚类图上,见图1。 "
根据d Score降序排序,挑选出差异最显著的前10个基因是:Wnt16、Obfc1、Ufd1l、LOC100361067、Hhatl、Fxyd1、Psmc4、Tasp1、Mettl21c、Ufd1l,见表1。 2.2 GO分析结果 通过综合分析列出前10位的生物学过程,包括:biological_process,G蛋白偶联受体信号通路(G-protein coupled receptor signaling pathway),对药物的反应(response to drug),DNA依赖性转录(transcription DNA-dependent),DNA依赖性转录的正调节(positive regulation of transcription DNA-dependent),氧化还原过程(oxidation-reduction process),泛素依赖性蛋白分解代谢过程(ubiquitin-dependent protein catabolic process),凋亡过程(apoptotic process),RNA聚合酶转录的正调控(positive regulation of transcription from RNA polymeras),脂肪酸β-氧化(fatty acid beta-oxidation)。见表2。 2.3 通路分析结果 作者分析出85条差异调控的通路。其中,差异最显著的10个通路分别是MAPK信号通路(MAPK signaling pathway)、细胞凋亡(Apoptosis)、柠檬酸循环(Citrate cycle)、癌症通路(Pathways in cancer)、细胞周期(Cell cycle)、丙酮酸代谢(Pyruvate metabolism)、Wnt信号通路(Wnt signaling pathway)、p53信号通路(p53 signaling pathway)、脂肪酸降解(Fatty acid degradation)、泛素介导的蛋白水解(Ubiquitin mediated proteolysis)。见表3。 "