Here's a transcriptome of a non-model organism. Comparing two conditions, kallisto generated ~6000 differentially expressed genes. KEGG metabolic pathways of a relative organism were used to classify DEGs and check pathways enrichment. These categories are relatively small (3-100 genes/set). Whilst DEGs number is so high, sets with PADJ is quite small - 10-15 sets are truly enriched (padj = 0.05). Same situation is appearing when we applied Fisher test.
We're newbies in the field and it feels like we've missed something. What do we do wrong? Sorry if I've missed any details.