Fig 1.
Principal component analysis (PCA) of sample relationship.
Correlations between 12 hypothalamic sample mapped onto first two principal components of PCA analysis based on genome-wide expression profiles. Triangle nodes standard for sample of egg-laying anaphase (LA), square nodes for sample of brooding prophase (BP), circle nodes for sample of brooding metaphase (BM).
Table 1.
Characteristics of the sequence reads from 12 hypothalamic libraries in Muscovy duck.
Fig 2.
Statistical results, GO enrichment and KEGG enrichment of different expressed genes (DEGs).
(A) Histogram of DEGs in pairwise comparisons of three group. Red bar for up-regulated genes, green bar for down-regulated genes. (B) Venn diagrams of DEGs in pairwise comparisons of three group. (C) Top 20 significantly enriched Biological processes of GO enrichment of DEGs in three comparisons. (D) The significantly enriched KEGG pathways of DEGs in three comparisons.
Fig 3.
Validation of the gene expression profile by qPCR.
Plot of gene expression log2 ratios (LA vs BP, LA vs BM and BP vs BM) determined by the RNA-Seq (X-axis) and RT-qPCR (Y-axis) for 24 selected genes (S6 Table). Correlation between RNA-Seq and RT-qPCR was calculated by Pearson product moment correlation in pairwise comparisons of three stages. Each dot represents one tested gene and the plots present linear regression lines, P values and correlation coefficients (r).
Fig 4.
Overall patterns of differentially expressed genes and the representative profiles in reproductive stages of LA, BP and BM.
(A) Patters were plotted on the heatmap using Treeview. Red represents up-regulated genes while green represents down-regulated genes. Hierarchical clustering is shown on the left. All 8 expression profiles identified by Short Time-series Expression analysis are shown in the middle and the summarized representative profiles are shown on the right. (B) STEM analysis grouping of significant differentially-expressed genes into three temporal profile clusters.
Fig 5.
Protein-protein interaction (PPI) networks of DEGs.
Circle nodes for genes/proteins, pentagon for transcription factors, rectangle nodes for KEGG pathway or biological process. Nodes with a degree of connectivity greater than 5 were labeled and all nodes in S1 Fig were labeled. According to trend analysis, genes/proteins were colored in red (Cluster 1, representing up-regulation over time), green (Cluster 2, representing down-regulation over time) and gray (Cluster 3, gene expression changed in BP stage only). Interaction were show as solid lines between genes/proteins, edges of KEGG pathway/biological process in dashed lines.