2.8 Functional enrichment analysis
Functional enrichment analyses were carried out on genes with
differential expression between tissues for a given sampling method. An
over-representation analysis (ORA) was run in the WEB-based GEne SeT
AnaLysis Toolkit (WebGestalt; Liao et al. 2019) focusing on gene
ontology (GO) categories associated with biological processes (BP). The
gene lists of interest were genes with significantly (p<0.05)
greater expression in one tissue type versus another for a given
sampling method. Only genes with known orthologs in zebrafish
(Danio rerio ) were used because choosing an organism of interest
for a comparison is a requirement of ORA. The reference gene list for
all comparisons was all zebrafish protein coding genes. Heatmaps of
functionally enriched genes across sampling methods and tissue
comparisons were generated using the ggplot2 package in RStudio.