Table 1.
Primer sequences used for real-time RT-PCR.
Fig 1.
Differentially expressed genes (DEGs) at different stages of gestation compared to genes expressed on day (D) 12 of pregnancy in the uterine endometrium in pigs.
(A) Up-regulated genes specifically observed on D15, D30, D60, D90, D114, or stages over more than two different days compared to genes expressed on D12 of pregnancy were re-arranged according to their expression patterns in red. (B) Down-regulated genes specifically observed on D15, D30, D60, D90, D114, or stages over more than two different days compared to genes expressed on D12 of pregnancy were re-arranged according to their expression patterns in green.
Table 2.
Number of differentially expressed genes at different stage of gestation compared to the genes expressed on day (D) 12 of pregnancy (P) in the uterine endometrium in pigs.
Fig 2.
Clustering analysis of differentially expressed genes in the uterine endometrium during pregnancy in pigs.
Clustering analysis was performed using the Mfuzz package and dendrograms of each cluster are depicted. The fuzzy c-means (FCM) clustering algorithm, which is a part of the package, uses a soft partitioning clustering method that requires two main parameters (c = number of clusters, m = fuzzification parameter). In this analysis, the optimal values of c and m were derived by the iterative refinement procedure. Through this optimization, two parameters were calculated as c = 8 and m = 1.25. As a result, eight clusters were obtained. Yellow or green lines correspond to genes with a low membership value; red and purple lines correspond to genes with a high membership value. Most genes included in this figure showed a high membership value.
Table 3.
List of enriched functional annotation groups in 8 clusters by functional annotation clustering analysis.
Fig 3.
Network analysis of gene expression in the porcine uterine endometrium during pregnancy to identify distinct modules of weighted coexpressed genes.
(A) Dendrograms produced by average linkage hierarchical clustering of 24,123 genes based on topology overlap. The red line indicates the height at which the tree was cut (0.94, red line) to define the module. Different modules were assigned colors as indicated in the horizontal bar beneath the dendrogram. (B) Heatmap images of all genes involved in 5 network modules. Columns represent probe identifications and putative annotations, and rows represent day of pregnancy. Red indicates high levels of expression and green indicates low levels of expression.
Table 4.
List of hub genes that have high connectivity in each module from weighted gene co-expression network analysis.
Fig 4.
Real-time RT-PCR analysis to technically validate hub genes and correlated genes.
(A) Heatmap with hierarchical clustering using 2-ΔΔCT values of 10 genes in real-time RT-PCR. (B) Correlation-based network plot. The edges represent significant correlation (FDR adjusted P-values < 0.05 in Pearson correlation test), and green and red colors represent positive and negative correlation, respectively.