Table 2. Number of differentially expressed genes and their pathway and GO term enrichment for PMN_HITTIN and PMN_HIT in response to Mtb.

Contrast	DEGsa	# Genes FDRb ≤ 0.05	# combined terms	KEGG	Reactome	GO BPc
				FDR≤ 0.1	FDR ≤ 0.1	FDR ≤ 0.1
PMNHIT d 6 hours(h) infected vs uninfected	Total	7610	701	65	15	621
	Upregulated	3816	915	53	51	811
	Downregulated	3794	10	0	10	0
PMNHITTIN e 6h infected vs uninfected	Total	6654	498	51	16	431
	Upregulated	3106	769	54	30	685
	Downregulated	3548	7	0	6	1
PMNHITTIN—PMNHIT 6h infectedf	Totalg	2285	496	111	86	299
	Less Upregulatedh	1217	719	48	55	616
	Less Downregulatedi	1068	29	13	12	4

^a DEGs (Differentially expressed genes)

^b FDR (false discovery rate)

^c GO BP (Gene Ontology Biological Processes)

^d PMN_HIT (HIV-1-infected IGRA positive tuberculin positive)

^e PMN_HITTIN (neutrophils from HIV-1-infected persistently TB, tuberculin and IGRA negative)

^f Refers to the interaction test looking at the difference in response to Mtb infection after 6h between PMN_HITTIN and PMN_HIT

^g Refers to combined responses with significant positive and negative log₂ fold change (log₂FC) from the interaction test

^{h, i} Refers to the negative^h and positiveⁱ log₂FC results from the interaction test