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. 2021 Dec 18;22(1):57.
doi: 10.1186/s12863-021-01014-w.

Identifying the hub genes for Duchenne muscular dystrophy and Becker muscular dystrophy by weighted correlation network analysis

Junjie Wang  1 , Qin Fan  1 , Tengbo Yu  2   3 , Yingze Zhang  4   5   6
Affiliations

Identifying the hub genes for Duchenne muscular dystrophy and Becker muscular dystrophy by weighted correlation network analysis

Junjie Wang et al. BMC Genom Data. .

Abstract

Background: The goal of this study is to identify the hub genes for Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) via weighted correlation network analysis (WGCNA).

Methods: The gene expression profile of vastus lateralis biopsy samples obtained in 17 patients with DMD, 11 patients with BMD and 6 healthy individuals was downloaded from the Gene Expression Omnibus (GEO) database (GSE109178). After obtaining different expressed genes (DEGs) via GEO2R, WGCNA was conducted using R package, modules and genes that highly associated with DMD, BMD, and their age or pathology were screened. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis and protein-protein interaction (PPI) network analysis were also conducted. Hub genes and highly correlated clustered genes were identified using Search Tool for the Retrieval of Interacting Genes (STRING) and Cystoscape software.

Results: One thousand four hundred seventy DEGs were identified between DMD and control, with 1281 upregulated and 189 downregulated DEGs. Four hundred and twenty DEGs were found between BMD and control, with 157 upregulated and 263 upregulated DEGs. Fourteen modules with different colors were identified for DMD vs control, and 7 modules with different colors were identified for BMD vs control. Ten hub genes were summarized for DMD and BMD respectively, 5 hub genes were summarized for BMD age, 5 and 3 highly correlated clustered genes were summarized for DMD age and BMD pathology, respectively. In addition, 20 GO enrichments were found to be involved in DMD, 3 GO enrichments were found to be involved in BMD, 3 GO enrichments were found to be involved in BMD age.

Conclusion: In DMD, several hub genes were identified: C3AR1, TLR7, IRF8, FYB and CD33(immune and inflammation associated genes), TYROBP, PLEK, AIF1(actin reorganization associated genes), LAPTM5 and NT5E(cell death and arterial calcification associated genes, respectively). In BMD, a number of hub genes were identified: LOX, ELN, PLEK, IKZF1, CTSK, THBS2, ADAMTS2, COL5A1(extracellular matrix associated genes), BCL2L1 and CDK2(cell cycle associated genes).

Keywords: Becker muscular dystrophy; Duchenne muscular dystrophy; Gene expression omnibus; Weighted correlation network analysis.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Results of normalization of dataset. a DMD vs control; b BMD vs control
Fig. 2
Fig. 2
Volcano plots of all DEGs. a DMD vs control; b BMD vs control
Fig. 3
Fig. 3
Determination of the soft-threshold powers (β). a DMD vs control; b BMD vs control
Fig. 4
Fig. 4
The clustering dendrogram of DEGs, non-clustering DEGs were shown in grey. a DMD vs control; b BMD vs control
Fig. 5
Fig. 5
Module-trait relationships. a DMD vs control; b BMD vs control
Fig. 6
Fig. 6
GO enrichment analysis of the highly correlated clustered DEGs. a DMD vs control; b BMD vs control
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