Fig. 3

Genes with shortened 3’UTRs are more likely to have upregulated expression. a Gene expression changes at different stages of spermatogenesis. Genes were divided into three groups based on 3’UTR regulation between comparing samples (FDR = 5 %, SAAP analysis), namely shortened, unchanged and lengthened (shown in blue, gray and red, respectively). 3’READS data were used for the analysis, with all APA isoforms of a gene combined to represent the overall expression of the gene. The median value for each group is indicated by a dotted vertical line. P values (K–S test) indicating difference in expression between genes with shortened or lengthened 3’UTRs and genes with 3’UTRs unchanged are shown in each graph (in blue or red, respectively). b Gene expression changes between different stages of spermatogenesis based on RNA-seq reads [NCBI GEO:GSE42004] mapped to coding sequences (CDS). Because only CDS reads were used, gene expression analysis was not affected by 3’UTR changes. As in (a), genes were divided into three groups based on APA regulation using 3’READS data with the closest time points. Dpp, day post partum. c Gene expression levels (log2(RPKM)) for genes with shortened, unchanged or lengthened 3’UTRs at different stages of spermatogenesis. The plot is based on the RNA-seq data used for (b). 3’UTR regulation is based on 4w vs. 2w comparison. d Testis-specific genes tend to have greater 3’UTR shortening than ubiquitously expressed genes. The number of genes for each group is indicated. The P value (K–S test) indicates difference in relative expression difference (RED, 4w vs. 2w, see Fig. 1f for definition) between two groups