Figure 2

Transcriptomic Analysis of the Chorioallantois (CA) from Mares with Nocardioform Placentitis. A Violin plot showing transcripts’ FPKM distribution in CA in control (CRL), nocardioform placentitis lesion (NPL), and nocardioform placentitis normal region (NPN) sets. The plots display the distribution of the data using kernel density plots (outer shapes). The inner horizontal lines show the interquartile range (the two outer thin lines), the median (the central thick line). B Principal component analysis (PCA) of the equine CA transcriptome from mares in CRL, NPN, and NPL sets. C Heat map of differentially expressed genes (DEGs; FDR < 0.05) in NPL vs. CRL, NPL vs. NPN, and NPN vs. CRL sets. The heat map was created using the normalized FPKMs of the DEGs (log10 [FPKM of the DEG + 1]). Normalized expression values are indicated on a color scale with red indicating high expression (positive z-score) and green indicating low expression (negative z-score). The circles at the bottom indicate the sample group (green = CRL, yellow = NPN, and red = NPL). The heat map was generated using the R package “heatmap.2”. D Venn diagram representing DEGs in common between NPL vs. CRL, NPL vs. NPN, and NPN vs. CRL sets. E UpSet diagram illustrating the intersection between DEGs (upregulated and downregulated) in NPL vs. CRL, NPL vs. NPN, and NPN vs. CRL sets. The nature of each intersection is indicated by the dots below the vertical bar plot. The vertical bars show the number of DEGs in each intersection, while the horizontal bars show the number of DEGs in each comparison. Key; CRL; normal postpartum (control), NPL; nocardioform placentitis lesion, and NPN; nocardioform placentitis normal region.