hnRNP C-TE binding sites repress genes similarly to nonrepetitive sites. (A) Genes targeted by hnRNP C were upregulated after hnRNP C knockdown (KD) compared to unbound genes, shown here as the cumulative distributions of the Cuffdiff differential expression test statistic (CDF). Positive values indicated greater abundance in the knockdown. (B) The test statistic distribution, plotted as the median and interquartile range, increased with the number of binding sites identified in the gene span. (C) Genes targeted only in TE sites were upregulated similarly to genes targeted only in nonrepetitive sites. The Venn diagram indicates the wide scale of TE binding sites, depicting the number of genes bound only in TEs, only in non-TEs, and in both. (D) A linear regression on the logarithm of the number of sites in each class showed that upregulation had a positive relationship with site number for all categories. Error bars represent a 95% confidence interval. The TE exon coefficient has large error bars because there were few examples to learn from.