Figure 4. Differential transcript abundance associated with TE variant presence/absence.
(A) Transcript abundance differences for genes associated with TE insertion variants at different positions, indicated in the plot titles. Genes with significantly different transcript abundance in accessions with a TE insertion compared to accessions without a TE insertion are colored blue (lower transcript abundance in accessions containing TE insertion) or red (higher transcript abundance in accessions containing TE insertion). Vertical lines indicate ±2 fold change in FPKM. Horizontal line indicates the 1% false discovery rate. (B) Relationship between rare TE variant counts and gene expression rank. Cumulative number of rare TE variants in equal-sized bins for gene expression ranks, from the lowest-ranked accession (left) to the highest-ranked accession (right). Lines indicate the fit of a quadratic model.
DOI: http://dx.doi.org/10.7554/eLife.20777.025
Figure 4—figure supplement 1. Relationship between rare TE variants and gene expression rank as for Figure 4B for permuted TE variants.
Figure 4—figure supplement 2. Relationship between rare TE variants and gene expression rank as for Figure 4B for TE insertions and TE deletions separately.
