Expression Profile of Genes Encoding Proteins Involved in Regulation of Vasculature Development and Heart Muscle Morphogenesis—A Transcriptomic Approach Based on a Porcine Model

Figures

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  Figure 1. Changes in right atrial appendage (RAA) cells morphology during long-term in vitro primary culture at individual time intervals. D: day of culture; 10×, 20×: magnification.

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  Figure 2. Changes in right atrium (RA) cells morphology during long-term in vitro primary culture at individual time intervals. D: day of culture; 10×, 20×: magnification.

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  Figure 3. Principal component analysis (PCA) plot of all differentially expressed genes (DEGs), based on the first two principal components (PC1 and PC2) loadings against each other. Percentage of variance is given in brackets.

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  Figure 4. Heatmaps with hierarchical clusterization of the differentially expressed genes, both in right atrial appendage (RAA) and right atrium (RA), belonging to “angiogenesis”, “blood vessel morphogenesis”, “circulatory system development”, “regulation of vasculature development”, and “vasculature development” GO BP terms. Each separate row on the y-axis represents a single transcript. Normalized signal intensity acquired from the microarray analysis is represented by color (green = higher expression; red = lower expression).

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  Figure 5. The representation of the mutual relationship between genes that belong to “angiogenesis”, “blood vessel morphogenesis”, “circulatory system development”, “regulation of vasculature development”, and “vasculature development” GO BP terms. The ribbons show the genes belonging to the given categories. The color bars near each gene correspond to logFC between culture intervals.

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  Figure 6. The circle plot showing the differently expressed genes and z-score of the GO BP terms of interest. The outer circle shows a scatter plot for each term of the fold change of the assigned genes. The inner circle shows the z-score of each GO BP term. The width of each bar corresponds to the number of genes within a GO BP term, and the color corresponds to the z-score.

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  Figure 7. The representation of hierarchical clusterization, FC and assignment of differently expressed genes that belong to “angiogenesis”, “blood vessel morphogenesis”, “circulatory system development”, “regulation of vasculature development”, and “vasculature development” GO BP terms. Genes are grouped together based on their expression patterns, and the clusterization pattern is represented by dendrogram inside the circle. The middle ring represents the logarithm of gene expression FC of studied genes. The outer ring represents the terms assigned to the genes. The genes were clustered based on their logFC values.

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  Figure 8. Venn diagram. The 50 most altered genes for RAA and RA were used in the comparison. Blue squares show downregulated genes, whereas red circles—upregulated.

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  Figure 9. RT-qPCR quantitative validation of microarray results presented in a form of a bar graph. The graph shows the relative changes in gene expression results for three different periods of cell culture (days: 7, 15 and 30) in relation to transcript levels obtained from cells before cultivation. All of the presented sample means were deemed to be statistically significant (p < 0.05).

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  Figure 10. The “signaling pathways regulating pluripotency of stem cells” KEGG pathway analysis of differentially expressed genes. The green and red colors indicate, respectively, upregulated and downregulated gene expression in the relevant comparisons. The boxes with gene names were separated into three parts containing the representation of mRNA expression from the 7th, 15th and 30th day of culture for right atrial appendage (RAA).

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  Figure 11. The “hypertrophic cardiomyopathy” KEGG pathway analysis of differentially expressed genes. The green and red colors indicate, respectively, upregulated and downregulated gene expression in the relevant comparisons. The boxes with gene names were separated into three parts containing the representation of mRNA expression from the 7th, 15th and 30th day of culture for right atrial appendage (RAA).