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Fig. 3 | BMC Plant Biology

Fig. 3

From: Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Fig. 3

Distributions of TE-related but also non-TE transcript expression differ between B73 and rpd1/rmr6 mutant. Frequency of transcripts with 0 FPKM (left), histograms of expression distribution (center) and cumulative frequency (right) for transcripts with >0 FPKM are reported for the previously classified high-confident-TEs (HC-TEs; a), putative/relics-TEs (pr-TEs; b) and non-TE transcripts (c). For all three groups, the frequency of transcripts with no expression (0 FPKM) in one genotype is significantly higher in B73 than in rpd1/rmr6 (P = 0, by Fisher’s exact test). The distributions of transcript expression are statistically different between the two genotypes for HC-TEs and non-TE transcripts (P < 0.01 by K-S test). Expression value plots for HC-TE transcripts subdivided in super-families (d) indicate higher expression in rpd1/rmr6 than B73 for RLC-Copia and RLG-Gypsy related transcripts (**: p < 0.01; Mann-Whitney U), while remaining super-families show comparable expression levels in the two genotypes. The boxes indicate the first quartile (bottom range) and third quartile (upper line) and are intersected by a crossbar corresponding to the median of the dataset. The whiskers represent the data that are within the 10th - 90th percentile and single dots depict the outliers

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