Data mining and bioinformatics analysis of expression profile chip for embryonic and mature mice liver
LYU Xing1 YANG Shuhong2
1.Department of General Surgery, Taikang Tongji (Wuhan) Hospital, Hubei Province, Wuhan 430050, China;
2.Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province, Wuhan, 430030, China
Abstract：Objective To depth analysis of liver differential expression genes in embryonic and mature mice. Methods Download gene expression profile data numbered GSE65063 from the National Center for Biotechnology Information (NCBI) GEO database, microchips were extracted at 14 embryonic days and 56 postnatal days. Online analysis tool GEO2R was used to complete differentially expressed genes (DEGs) screening. DAVID was used to analyze the gene ontology and Kyoto Encyclopedia of Genes and Genomes biological pathway enrichment of DEGs, STRING was used to analyze the interaction between proteins encoded by DEGs, visualization with Cytoscape software. MCODE loaded in Cytoscape software was used to build functional modules, CytoHubba was used to screen the hub genes and analyze them to construct PPI network map. Results A total of 2969 DEGs were screened in mature liver compared with embryonic liver, of which 1620 were up-regulated and 1349 were down-regulated. Upregulated DEGs were mainly concentrated in metabolism-related biological processes, organelle components and metabolic pathways, while down-regulated DEGs were mainly concentrated in cell cycle, DNA repair and other cell proliferation-related organelles, biological processes and signaling pathways. Modular analysis showed that the top gene modules were all down-regulated genes, which were mainly enriched in signaling pathways related to cell cycle and cell senescence. Module two was mainly related to complement system, cholesterol metabolism and PARP signaling pathway. Module third was mainly related to retinol metabolism steroid and somatic hormone synthesis. A total of 16 hub genes were screened out, among which 14 were down-regulated and two were up-regulated. Conclusion There are significant differences in gene expression profiles between matare and embryonic liver maturation and embryonic stage. Liver development and maturation are regulated by specific gene groups in different time and space. Metabolism-related genes are dominant in mature liver, while cell proliferation and division related genes are mainly concentrated in embryonic liver. The screened hub genes, especially the down-regulated genes, may be used as early diagnostic and prognostic indicators for liver abnormalities such as liver cancer, which is of great clinical significance.
吕兴1 杨书红2. 小鼠胚胎期与成熟期肝脏表达谱芯片数据挖掘及生物信息学分析[J]. 中国医药导报, 2021, 18(4): 4-8,28.
LYU Xing1 YANG Shuhong2. Data mining and bioinformatics analysis of expression profile chip for embryonic and mature mice liver. 中国医药导报, 2021, 18(4): 4-8,28.
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2021, Vol. 18 
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