Table 2.

Enrichment analysis for biological process and KEGG pathways.

Days post Rx initiation	GO term	Count	p-value	Fold enrichment	FDR
Effective treatment: downregulation
Rx-1D	Growth	34	5.60E–04	1.7	3.40E–02
	Response to hypoxia	11	2.90E–06	6.6	3.50E–04
	Pathogenesis	13	1.10E–03	2.9	4.40E–02
Rx-3D	Growth	93	7.60E–09	1.7	1.80E–06
	Pathogenesis	34	4.40E–08	2.7	5.20E–06
	Protein secretion by the type VII secretion system	7	1.00E–04	7.4	7.10E–03
	Response to heat	8	1.20E–04	6	7.10E–03
Rx-5D	Translation	32	2.20E–06	2.3	6.40E–04
	Growth	161	3.10E–06	1.3	6.40E–04
	Response to hypoxia	25	6.90E–06	2.5	9.60E–04
Rx-7D	Growth	44	6.50E–06	1.8	1.00E–03
	Response to hypoxia	9	6.00E–04	4.5	4.80E–02
Rx-14D	Protein secretion by the type VII secretion system	5	6.30E–05	19.9	5.70E–03
KEGG pathway
Rx-5D	Ribosome	33	5.20E–09	2.7	4.80E–07
Effective treatment: upregulation
KEGG pathway
Rx-5D	ABC transporters	24	4.40E–05	2.4	4.00E–03
Ineffective treatment: upregulation
KEGG pathway
Rx-7D	Biosynthesis of antibiotics	5	2.40E–03	4.50	4.20E–02

Enrichment of genes in biological process and KEGG²⁶ pathway was performed using the functional annotation tool of the Database for Annotation, Visualization, and Integrated Discovery (DAVID) web interface v 6.8²⁷. Rx- Treatment, Rx-1D to Rx-14D – days post-treatment initiation, p-Value < 0.05 considered significant, FDR false discovery rate.