Fig. 2

Overview of TEs in the genome and various conditions. a The proportion of all TEs in various genomic compartments. The allocation of TEs obeys this priority: CDS exons > UTR exons > Introns > Intergenic regions. b The expression summary of TE subfamilies in all groups. This panel can be divided into the left and right sides. Right sides from outside to inside represent organ and four developmental stages in both sexes. Green represents 2-week-old rats. Red represents 6-week-old rats. Blue represents 21-week-old rats. Yellow represents 104-week-old rats. Light color represents male and dark color represents female. So, right sides contain 80 groups. Left sides from outside to inside represent TE class and relation with organs, developmental stages and sexes. In internal layer, red represents commonly expressed TEs; gray represents zeros expressed TEs; yellow represents hub TEs and blue represents non-hub TEs. In order to visualize, the relations between commonly expressed TEs and organs were not drawn. A line represents that a TEs expressed in a group. c The proportion of subfamily types that simply expressed in each TE class in 11 organs. For comparison, “Background” TEs represent those simply found in the genome. d Hierarchical cluster analysis of TE subfamily expression signals across 320 samples. The row represents TEs, and the column represents samples. e The relative contribution was calculated by PVCA, including main effects (organ, age, sex and replicate) and their combinations