Novel Genes Involved in Hypertrophic Cardiomyopathy: Data of Transcriptome and Methylome Profiling

Figures

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  Figure 1. Visualization of the DEGs identified in the LV myocardial tissue of HCM patients when compared to AS patients. (A): Volcano plot of gene expression levels. Blue vertical lines indicate threshold for expression differences |log2FC| = 1; blue horizontal line—threshold for statistical significance (padj = 0.05). Significantly downregulated genes (padj < 0.05, log2FC < −1) are marked in red; significantly upregulated genes (padj < 0.05, log2FC > 1)—in green; genes with padj < 0.05 that do not exceed the threshold |log2FC| = 1—in gray. (B): Heatmap of z-scored expression levels of 193 identified DEGs in all studied patients. Decreased expression levels of DEGs are marked in red, and increased levels—in green. Top dendrogram shows hierarchical clustering of RNA samples. Cyan indicates RNA samples from HCM patients; pink—from AS patients.

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  Figure 2. Visualization of the DMPs identified in LV myocardial tissue of HCM patients when compared to AS patients. (A): Volcano plot of all CpG site methylation levels. Red vertical lines indicate threshold for methylation differences (|deltaBeta| = 0.05); red horizontal line—threshold for statistical significance (p = 0.01). DMPs passing both thresholds are marked on the figure with blue dots (hypomethylated in HCM) and yellow dots (hypermethylated in HCM). (B): Heatmap of z-scored methylation levels of 1755 identified DMPs in all studied patients. Methylation level varies from fully unmethylated (blue) to fully methylated (yellow). Top dendrogram shows hierarchical clustering of DNA samples. Cyan indicates DNA samples from HCM patients; pink—from AS patients.

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  Figure 3. Correlation of expression of 14 DEGs with methylation levels of 17 neighboring DMPs. Cyan and pink dots represent HCM and AS patients, respectively. The black regression line and its confidential interval (gray area) are shown on each plot. Spearman’s rank correlation coefficients and p-values calculated for each of the 17 DEG–DMP pairs are presented above corresponding dot plots. Significant coefficients and p-values are marked in bold. Location of DMPs according to gene functional elements and CpG landmarks are indicated under each plot. TSS1500 and TSS200—regions within 1500-200 and 200-0 nucleotides upstream from the transcription start site (TSS), respectively; 5’UTR and 3’UTR—5′ and 3′ untranslated regions, respectively. NS—not significant.

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  Figure 4. Expression levels of NOTCH3, GADD45G, GIGYF1, SLC17A7, and CBFA2T3 in 13 HCM patients and 14 AS patients, as determined via RT-qPCR. RNA levels were calculated relative to GAPDH. The data are presented using a scatter plot (median with interquartile ranges). The differences in RNA levels between HCM patients and AS patients were considered to be significant if the p-value in the Mann–Whitney U test was less than 0.05.

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  Figure 5. Visualization of GO terms overrepresented by DEGs and DMP-containing genes. Top left Euler-Venn diagram schematically represents sets of identified GO terms enriched with DMP-containing genes (orange) or with DEGs (blue) and their overlap (green). TreeMap diagrams show REVIGO clasterization of the identified GO term sets by similarity. Each colored rectangle on the map represents one GO term; the size of the rectangle indicates the ‘uniqueness’ of the GO term—the negative of its average similarity to all other input terms. Groups of similar processes forming the cluster are marked with the same color.