Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase

Figures

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  Fig 1. Volcano plot of gene expression changes in DCM patients undergoing heart transplant versus donors. RNA sequencing data from left ventricle heart tissue of GEO dataset GSE141910 was used for foldchange analysis with DESeq2 R package. The volcano plot was created using EnhancedVolcano. The X-axis shows the log2FoldChange and the Y-axis shows the -log10 of p value. Red color shows genes that are significantly changed (log2FoldChange> = 1, or < = -1, and p<0.01). Blue color shows genes that had more than or equal to two-fold change, but p> = 0.01. Black color shows genes that have less than two-fold change and p> = 0.01.

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  Fig 2. Gene ontology (GO) analysis of differentially expressed genes in DCM patients versus donors. Differentially expressed genes (DEGs) were derived from DESeq2 analysis that had more than or equal to two-fold changes in DCM patients versus donors. The GO analysis was performed using the web based Enrichr program. The figures of overrepresented pathways in GO biological process, molecular function, and cellular component were created by Appyter, an enrichment analysis visualizer.

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  Fig 3. KEGG pathway analysis in DCM patients versus donors. The whole gene set of log2FoldChange data from DCM patients versus donors were uploaded to the web based GSEA analysis program (webgestalt.org) for KEGG analysis. The top 10 upregulated (blue) and downregulated (orange) pathways are presented in the figure. FDR, false discovery rate. FDR<0.05 indicates significant change.

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  Fig 4. Relationship of gene modules and clinical phenotypes. The weighted gene co-expression network analysis (WGCNA) was performed with the published dataset of GSE141910 using the WGCNA R package. The correlation coefficients of each gene module and corresponding clinical phenotype were calculated and displayed as a heatmap as shown in the right panel of the figure. The green color indicates a negative correlation and red color indicates a positive correlation between modules and phenotypes. The p values are shown in parentheses under each coefficient number. Gene modules were analyzed and presented in different colors as shown on the left side of the heatmap, and the clinical phenotypes were shown at the bottom of the heatmap. The left panel is a String analysis showing the potential protein-protein interactions between the genes that included the top gene modules corresponding to each phenotype. The colors in the String network indicate each clinical phenotype and corresponding gene modules listed in the center of the figure.

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  Fig 5. Consensus analysis of African Americans (AA) and Caucasians (CA) in the cohort of GSE 141910. (A): Consensus gene dendrogram and module colors using data from African Americans and Caucasians. The consensus gene dendrogram was obtained by average linkage using a pair-wise weighted correlation metric, and clustered according to a topological overlap metric into modules. Assigned modules were colored at the bottom. (B): Summary plot of consensus eigengene networks and their differential analysis from AA and CA groups. The top panels showed the clustering of consensus eigengenes in the two groups. The heat maps in the middle and bottom panel showed the correlation of eigengene network between the two groups, and the bar graph in the middle panel showed the mean preservation of adjacency for each eigengene to other eigengenes. The D value was calculated as the arithmetic mean of these measurements.

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  Fig 6. Gene expression and signaling pathway changes in African American (AA) and Caucasian (CA) in DCM patients versus donors. The log2FoldChange data from AA and CA groups were derived from DESeq2 R program and separately used for KEGG pathway analysis. The top 10 upregulated and downregulated pathways in each group were presented in the figure. FDR, false discovery rate. FDR<0.05 indicates significant change.

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  Fig 7. Relationship between Na/K-ATPase gene expression and heart function. The correlation between Na/K-ATPase α1, α2, and α3 gene expression and left ventricle ejection fraction (LVEF) was analyzed and presented in the figure. The scatter plot was created using GraphPad, and linear regression curves with 95% confidence (shadowed area) are shown in blue. Gene expression data of Na/K-ATPase (α1, α2, α3) genes and LVEF were obtained from published dataset (GSE141910).

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  Fig 8. Mapping of gene expression change on Na/K-ATPase/Src signaling pathway. The log2FoldChange data from DCM patients versus donors and the corresponding gene names were mapped to the Na/K-ATPase/Src signaling pathway (Wikipathway WP5051) using Cytoscape. The log2FoldChange data were presented as continuous colors. The blue color indicates a downregulation and red color indicates an upregulation of the gene.