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中华妇幼临床医学杂志(电子版)

Chinese Journal of Obstetrics & Gynecology and Pediatrics(Electronic Edition) ›› 2020, Vol. 16 ›› Issue (05): 551 -557. doi: 10.3877/cma.j.issn.1673-5250.2020.05.008

Special Issue: ；

Original Article

Screening and bioinformatics analysis of differentially expressed genes in unexplained recurrent spontaneous abortion based on the GEO database

Hengxi Chen1, Shuting Cheng2, Li Xiao1, Wei Huang1,†()   

  1. 1. Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
    2. West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan Province, China
  • Received:2019-10-01 Revised:2020-08-01 Published:2020-10-01
  • Corresponding author: Wei Huang
  • Supported by:
    Key Research and Development Program of Science and Technology Department of Sichuan Province(2019YFS0421)
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Objective

To screen the differentially expressed genes in endometrial of patients diagnosed with unexplained recurrent spontaneous abortion (URSA) and explore the related pathways and biological processes.

Methods

This study was searched using " recurrent sporadic abortion" , " recurrent probability loss" , " endometrium" and " homo sapiens" as the search key words. The R language was used to analyze the microarray data, screen the differential genes, and intersect the differential genes between the datasets to obtain co-differentially expressed genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways of co-differentially expressed genes were enriched using the David database. The protein-protein interaction (PPI) network of co-differentially expressed genes encoding proteins in the data set was constructed by using STRING database, and visualized by using Cytoscape software (v3.0).

Results

①Two data sets, GSE26787 and GSE65099, were obtained in this study. Then, the difference genes of the two data sets were intersected, and finally 23 co-differentially expressed genes were screened. Among these 23 co-differentially expressed genes, there were 19 up-regulated genes (ADM2, SH3D21, FGFR4, SULT2B1, NRG2, SERPINA4, NLRP5, FAM124B, MCOLN3, SLC7A1, PPP1R1B, SQLE, SLC24A4, PLPPR5, EPHB3, SMIM24, ZNF589, SOX7, EDN3) and 4 down-regulated genes (PRKCB, ANG, IRX5, ATG9B). ②The Go enrichment analysis of co-differentially expressed genes obtained 3 parts including BP, CC and MF. Co-differential expressed genes of BP were mainly related to cellular calcium ion homeostasis, angiogenesis, and intracellular signal transduction. CC mainly involved the whole composition of the membrane; MF mainly involved receptor binding. ③KEGG pathway enrichment analysis showed that co-differentially expressed genes were enriched in ErbB signaling pathway (P=0.070, FDR=55.245). Co-differentially expressed genes involved in ErbB signaling pathway were NRG2 and PRKCB.

Conclusions

Some differentially expressed genes can be effectively screened by bioinformatics analysis, and it can provide the basis for further research.

Key words: Endometrium, Gene expression, Abortion, habitual, Abortion, spontaneous, Biological processes, Women
图1 GSE26787数据集差异表达基因热图
图2 GSE65099数据集差异表达基因热图
表1 GO富集分析共同差异基因
类型 GO序号 注释 P值 FDR 基因
BP 0006874 细胞Ca2＋稳态 0.002 2.676 EDN3、SLC24A4、PRKCB
  0001525 血管生成 0.010 11.174 ANG、ADM2、EPHB3
  0035556 细胞内信号传导 0.039 37.232 PPP1R1B、NRG2、PRKCB
CC 0005887 膜的整体组分 0.019 15.398 FGFR4、SLC24A4、SLC7A1、PLPPR5、EPHB3
MF 0005102 受体结合 0.090 62.059 ANG、NRG2
图3 GSE26787和GSE65099数据集差异基因PPI网络图
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