Fig. 2
Downstream molecular impacts on global gene expression and regulation. A Box-and-whisker plot of module eigengene (ME) expression for the differentially expressed module. ME expression values have significantly different means (t = 2.1348, df = 19.744, p = 0.0455) between samples containing the ancestral and derived TE genotypes at GTF2I. Whiskers represent the data range excluding outliers. Horizontal edges correspond to 25th, 50th and 75th percentiles. B Gene ontology (GO) hits for genes in the differentially expressed module displaying their -log10p for each GO categories: Molecular Function (MF), Biological Processes (BP), Cellular Component (CC), Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) and Human Phenotype (HP). Top GO term in each category is numbered and keyed. C Volcano plot of differentially expressed genes (red points; FDR < 0.1, or p < 0.001 and log2 fold change >|2|), for the 22 samples. D Spiked-in normalized read counts for E2F1 enrichment and; E H3K27ac marks. Bar heights represent mean values, error bars correspond to standard errors, and black circles depict replicate values