Integrative Analysis of Blood Transcriptomics and Metabolomics Reveals Molecular Regulation of Backfat Thickness in Qinchuan Cattle

Figures

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  Figure 1. Basal analysis of the transcriptome and the different phenotypes profiles in the BFT (n = 8). (A) Comparison of the BFT phenotypes (** means p-value < 0.05). (B) The FPKM boxplot for each sample. (C) The heatmap of expression correlation between samples. (D) The principal component analysis (PCA). (E) Volcano plots of the DEGs in the BFT. (F) The GO annotation analysis histogram of DEGs for BFT. (G) The plot of the degree of KEGG pathway enrichment for DEGs. The vertical coordinates indicate the enriched pathway, and the horizontal coordinates indicate the value of the enrichment factor (ratio of the annotated DEGs to all genes in the enriched pathway). (H) FPKM of CRABP2 in the H and L groups. (I) FPKM of ZFP57 in the H and L groups (*** means p-value < 0.01).

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  Figure 2. The separate metabolome data analysis of the BFT. (A) The principal component analysis (PCA). (B) The partial-least-squares-discriminant analysis (OPLS-DA) score plots. (C) The volcano plots of the DEMs. (D) The cluster heatmap of the DEMs. (E) The plot of the differential metabolite KEGG enrichment. The x-axis is the ratio of the number of DEMs in the corresponding pathway to the total number of metabolites that were detected and annotated in the pathway. The y-axis is the pathway name. The color of the dots represents the log (p-value), with more red indicating a more significant enrichment. The size of the dots represents the number of differentially enriched metabolites.

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  Figure 3. Combined metabolome and transcriptome analysis. (A) Nine-quadrant diagrams. The calculation of correlations between all genes and metabolites based on the Pearson correlation, with screening thresholds of |CC| > 0.80 and CCP < 0.05. Left-to-right and top-to-bottom indicates the order of quadrants 1 to 9. The 3rd and 7th quadrants represent the same trend of gene and metabolite expression, which indicate that the genes may be positively regulated metabolites. The 1st and 9th quadrants indicate that the genes and metabolites are negatively correlated. The 2nd and 8th represent not just the unchanged genes but also the up- and down-regulation of the metabolites. The 4th and 6th represent not just the unchanged metabolites but also the genes that were up-regulated. The 5th indicated no significant changes in both the metabolites and the genes. Only quadrants 1, 2, 3, 7, 8, and 9 were involved in this analysis. (B) The correlation analysis hierarchical clustering heatmap. Each row of the hierarchical clustering heatmap represented one DEG or DEM for each column of that differentially grouped sample. The clusters appear in the same cluster of significantly different metabolites or…

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  Figure 4. Correlation and pathway analysis of the DEGs and DEMs. The ceramide metabolic process was assigned with four central DEGs and DEMs of the KEGG-rich pathway.