Using WGCNA to analyze changes of FMDV infection pathway in cattle

doi:10.3969/j.issn.1004-1524.2021.09.06

Acta Agriculturae Zhejiangensis ›› 2021, Vol. 33 ›› Issue (9): 1617-1624.DOI: 10.3969/j.issn.1004-1524.2021.09.06

• Animal Science • Previous Articles Next Articles

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

Abstract

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

CLC Number:

S858.23

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.

Figures/Tables 5

Fig.1 Screening of soft thresholds

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

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.

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

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

References 26

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Using WGCNA to analyze changes of FMDV infection pathway in cattle

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