1. GOrilla, REVIGO, GSEA
2. GOrilla: Not described; REVIGO: Not described; GSEA: Version 2.2.3
3. GO (Gene Ontology), MSigDB (specifically, tissue-specific TRM-associated gene sets)
4. Yes (tissue-specific TRM-associated gene sets)
5. Hypergeometric test (GOrilla), Fisher's exact test (Not explicitly stated, but implied by GOrilla), GSEA: weighted enrichment statistic
6. Yes