利用加权基因共表达网络分析牛口蹄疫病毒感染通路变化

doi:10.3969/j.issn.1004-1524.2021.09.06

浙江农业学报 ›› 2021, Vol. 33 ›› Issue (9): 1617-1624.DOI: 10.3969/j.issn.1004-1524.2021.09.06

利用加权基因共表达网络分析牛口蹄疫病毒感染通路变化

杨生海¹^,²(), 刘西兰², 张勇¹^,^*()

1.甘肃农业大学动物医学院,甘肃兰州 730070
2.中农威特生物科技股份有限公司,甘肃兰州 730046

收稿日期:2020-06-18 出版日期:2021-09-25 发布日期:2021-10-09
通讯作者: 张勇
作者简介:* 张勇,E-mail: zhychy@163.com
杨生海(1978—),男,甘肃庆阳人,博士研究生,副研究员,主要从事口蹄疫疫苗检验工作。E-mail: 916735787@qq.com
基金资助:
动物繁殖疾病防控协同创新团队(2018C-15)

Using WGCNA to analyze changes of FMDV infection pathway in cattle

YANG Shenghai¹^,²(), LIU Xilan², ZHANG Yong¹^,^*()

1. College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
2. China Agricultural Vet. Bio. Science and Technology Co., Ltd., Lanzhou 730046, China

Received:2020-06-18 Online:2021-09-25 Published:2021-10-09
Contact: ZHANG Yong

摘要/Abstract

摘要：

从基因表达综合数据库下载GSE83514数据集,利用加权基因共表达网络分析(WGCNA)筛选与牛口蹄疫病毒感染的相关模块及枢纽基因,并对整个模块内的基因进行GO功能注释和KEGG通路分析。结果显示,通过构建WGCNA共表达网络,确定与牛口蹄疫病毒感染显著负相关的Darkred模块和显著正相关的Green模块为枢纽模块,它们的枢纽基因分别为MFSD4和RHOH。这两个模块基因共富集到20个生物学过程及14条KEGG信号通路,并且两个模块同时富集到DNA复制通路。本研究为探究牛口蹄疫病毒感染通路变化提供了生物信息学依据,筛选的枢纽基因MFSD4和RHOH有望成为抑制牛口蹄疫病毒感染的治疗靶标。

关键词: 牛口蹄疫病毒, 转录组测序, 加权基因共表达, 数据挖掘, 枢纽基因

Abstract:

In this study, GSE83514 data set was downloaded from Gene Expression Omnibus (GEO) database, and Weighted Gene Co-Expression Network Analysis (WGCNA) was used to explore the related modules and hub genes of bovine foot-and-mouth disease virus (FMDV) infection. The results showed that through constructing WGCNA co-expression network, the genes of Darkred module and Green module were found to be negatively and positively related to bovine FMDV infection respectively. MFSD4 and RHOH were the hub gene of Darkred module and Green module, respectively. Twenty Gene Ontology (GO) terms and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched in those two modules. DNA replication signaling pathway was the only pathway enriched in both modules. The results of this study provided a bioinformatics basis for investigating the molecular mechanism of bovine FMDV infection, and the selected hub genes, MFSD4 and RHOH, were expected to be therapeutic biomarker for inhibiting the infection of FMDV.

Key words: foot-and-mouth disease virus of bovine, RNA-seq, weighted gene co-expression network analysis, data excavation, hub gene

中图分类号:

S858.23

杨生海, 刘西兰, 张勇. 利用加权基因共表达网络分析牛口蹄疫病毒感染通路变化[J]. 浙江农业学报, 2021, 33(9): 1617-1624.

YANG Shenghai, LIU Xilan, ZHANG Yong. Using WGCNA to analyze changes of FMDV infection pathway in cattle[J]. Acta Agriculturae Zhejiangensis, 2021, 33(9): 1617-1624.

图/表 5

图1 软阈值的筛选

Fig.1 Screening of soft thresholds

图2 基因聚类树与模块构建 A, 基因聚类树;B,动态树;C,动态树合并。

Fig.2 Gene clustering tree and module construction A, Cluster dendrogram; B, Dynamic tree cut; C, Merged dynamic.

图3 WGCNA结果模块内基因网络图及枢纽基因 A,模块基因与临床性状热图;B,Darkred模块基因相关性散点图;C,Green模块基因相关性散点图;D,Darkred模块基因网状图;E,Green模块基因网状图。

Fig.3 Results of WGCNA and hub gene in each module A, Heatmap of the correlation between module eigengenes and clinical traits; B, Scatter plot of module eigengenes in the Darkred module; C, Scatter plot of module eigengenes in the Green module; D,Network of genes in Darkred module; E, Network of genes in Green module.

图4 GO富集气泡图 A, Darkred模块GO富集结果;B,Green模块GO富集结果。

Fig.4 GO enrichment bubble diagram==140A, GO enrichment bubble diagram of Darkred module; B, GO enrichment bubble diagram of Green module.

图5 KEGG富集气泡图 A,Darkred模块KEGG富集结果;B,Green模块KEGG富集结果。

Fig.5 KEGG enrichment bubble diagram A, KEGG enrichment bubble diagram of Darkred module; B,KEGG enrichment bubble diagram of Green module.

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利用加权基因共表达网络分析牛口蹄疫病毒感染通路变化

Using WGCNA to analyze changes of FMDV infection pathway in cattle

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