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Fig. 4 | Journal of Experimental & Clinical Cancer Research

Fig. 4

From: Alcoholic fatty liver disease inhibited the co-expression of Fmo5 and PPARα to activate the NF-κB signaling pathway, thereby reducing liver injury via inducing gut microbiota disturbance

Fig. 4

Identification of DEGs, construction of PPI network, and WGCNA analysis. For GSE8006 dataset, a The heat map for DEGs. b The volcano plot for DEGs. Black dots represent genes which are not differentially expressed, left dots represent the upregulated genes, and the right dots represent the downregulated genes. c A PPI network of DEGs was visualized by Cytoscape software. d The top 10 hub genes were identified by the cytohubba plug-in of Cytoscape software. GO terms, including BP, CC, and MF were shown in (e). f KEGG enrichment analysis was shown based on DAVID database. For GSE40334 dataset, g The heat map for DEGs. h The volcano plot for DEGs. Black dots represent genes which are not differentially expressed, left dots represent the upregulated genes, and the right dots represent the downregulated genes. i A PPI network of DEGs was visualized by Cytoscape software. j The top 10 hub genes were identified by the cytohubba plug-in of Cytoscape software. GO terms, including BP, CC, and MF were shown in (k). l KEGG enrichment analysis was shown based on DAVID database. m One outlier (GSE8006) was detected by sample clustering; n analysis of the scale-free topology model fit index for soft threshold powers (β) and the mean connectivity for soft threshold powers; o A cluster dendrogram was built based on the dissimilarity of the topological overlap, which presents 31 gene co-expression modules in colon specific pathogen free group; Each designated color represents a certain gene module; p The module relationships and significance; q A PPI network of the hug genes from in the darkmagenta module was visualized by Cytoscape software; r The top 10 hub genes of this PPI network were identified by the cytohubba plug-in of Cytoscape software. s One outlier (GSE40334) was detected by sample clustering; t analysis of the scale-free topology model fit index for soft threshold powers (β) and the mean connectivity for soft threshold powers; u A cluster dendrogram was built based on the dissimilarity of the topological overlap, which presents 111 gene co-expression modules in colon specific pathogen free group; Each designated color represents a certain gene module; v The module relationships and significance; w A PPI network of the hug genes from in the darkturquoise module was visualized by Cytoscape software; x The top 10 hub genes of this PPI network were identified by the cytohubba plug-in of Cytoscape software

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