HeliScopeCAGE-based GO and pathway analyses. (A) Heatmap (log10 scaled) of significance values for GO enrichment terms related to biological processes. Enrichment for GO terms was calculated for subset-specific gene sets using DAVID tools.24 P values for enrichment of each GO term were calculated using the hypergeometric test and corrected for multiple hypothesis testing using the Benjamini-Hochberg procedure. Intensity of the red coloring indicates the significance of term enrichment. Only generic terms are given. (B) Relative HeliScopeCAGE-based gene expression levels of genes in enriched pathways. Symbols of subset-specific genes are provided for each pathway. Additional examples, including lysozyme, nucleotide oligomerization domain-like/Toll-like receptor–like receptor signaling pathway, antigen processing and presentation, ribosome, and protein metabolism are shown in supplemental Figure 6. Notably, the observed differences were independent of the normalization method and also observed using normalization to a fixed tag count (TPM) or relative log expression normalization (as provided by EdgeR) of raw tag counts.
