Additional file 1 of Regulatory signatures involved in the cell cycle pathway contribute to egg production heterosis in chicken

Additional file 1: Fig. S1 The summary of sample sequence statistics including clean reads, clean bases, Q20, Q30, GC content and overall mapping rate. Fig. S2 The PCA for transcriptome profiles of purebreds and crossbreds in each laying stage. Fig. S3 Scale independence and mean connectivity for purebreds and crossbreds using various soft threshold powers. Fig. S4 Venn diagram showing the overlapped GO terms enriched by EN-related module genes in each genetic group. Fig. S5 Pairwise module preservation of gene co-expression networks between the crossbreds and their parents. Dashed red and blue lines represent the Zsummary thresholds for strong (Zsummary > 10) and weak to moderate (2 < Zsummary < 10) preservation levels, respectively. Colored dots represent the corresponding modules in the reference network, and the module size is the number of overlapped genes within each reference module. Fig. S6 The cluster profiles of consensus modules (CMs) and group-specific modules for crossbred WY (a) and crossbred YW (b) compared to their parents, respectively. Fig. S7 The consensus and divergence of gene co-expression networks between the crossbred YW and its parents (WW and YY) during the 5 laying stages. (a) Hierarchical cluster dendrogram showing consensus gene co-expression modules (CMs) among WW, YY and YW. The red line above is the cut height (0.995) for CM identification. CM colors are labeled independent of the separately identified modules in each group. (b) The relationships between global and group specific co-expression networks. The vertical axis represents CMs. The horizontal axis represents modules within each group (c) The relationships among eigengenes of CMs in each group. (d) The expression patterns of eigengenes of CMs in WW, YY and YW during 5 laying stages. Blue and red represent lesser and greater expression, respectively. (e) Heatmap showing KEGG pathways significantly enriched by genes in each CM. Color intensity represents the significance of enrichment. Fig. S8. Hub genes in the preserved gene co-expression network underlying the dynamic egg production heterosis. (a) Upset plot showing the common hub genes among WW, YY and YW. (b) KEGG pathways enrichment analysis for the common hub genes. The color bar represents the ratio of gene numbers in each pathway, and the black dot represents the significance (adjusted P value) of the KEGG pathway. (c) The differential expression patterns during 5 laying stages for hub genes involved in the cell cycle. The cell colors represent differential expression patterns, and the colors on the left represent the corresponding CM and KEGG pathway to which each gene belongs, respectively.