TABLE 1.

Overlap of TNFα gene hallmark leading-edge subsets

Gene in subseta
Medium (RSTR down)		M. tuberculosis (RSTR up)
Uganda (33/98 LE genes)	South Africa (35/92 LE genes)	Uganda (37/96 LE genes)	South Africa (12/47 LE genes)
CCL20	CCL20	CCL20	CCL20
IL7R	IL7R	IL7R	IL7R
INHBA	INHBA	INHBA	INHBA
PTX3	PTX3	PTX3	PTX3
TNFAIP6	TNFAIP6	TNFAIP6	TNFAIP6
TNIP1	TNIP1	TNIP1	TNIP1
ABCA1	ABCA1	ABCA1
AREG	AREG	AREG
CCL4	CCL4	CCL4
CXCL1	CXCL1	CXCL1
CXCL2	CXCL2	CXCL2
CXCL3	CXCL3	CXCL3
DUSP2	DUSP2	DUSP2
DUSP4	DUSP4	DUSP4
EHD1	EHD1	EHD1
GPR183	GPR183	GPR183
HES1	HES1	HES1
IFIT2	IFIT2	IFIT2
	IL1B	IL1B	IL1B
IL23A	IL23A	IL23A
	MARCKS	MARCKS	MARCKS
NFKB2	NFKB2	NFKB2
NFKBIA	NFKBIA	NFKBIA
NR4A1	NR4A1	NR4A1
NR4A2	NR4A2	NR4A2
OLR1		OLR1	OLR1
PDE4B	PDE4B	PDE4B
PFKFB3	PFKFB3	PFKFB3
PNRC1	PNRC1	PNRC1
	PTGS2	PTGS2	PTGS2
	SLC2A6	SLC2A6	SLC2A6
SOCS3	SOCS3	SOCS3
SOD2	SOD2	SOD2
TNC		TNC	TNC
TNFAIP3	TNFAIP3	TNFAIP3
ZC3H12A	ZC3H12A	ZC3H12A
ZFP36	ZFP36	ZFP36

^aGenes are listed if they were members of the leading-edge (LE) subset in at least 3 of 4 gene set enrichment analyses (columns) using the hallmark “TNFα signaling via NF-κB” gene set (MsigDB). Expression of these LE genes was lower (medium condition) or higher (M. tuberculosis condition) in RSTR than in LTBI monocytes. Of the 200 genes in this gene set, the LE subset consisted of 98 genes (Uganda medium), 92 genes (South Africa medium), 96 genes (Uganda M. tuberculosis), and 47 genes (South Africa M. tuberculosis) in the respective analyses. Gene order is alphabetical, and genes are grouped by overlap across all 4 analyses (above line) or 3 of 4 analyses (below line). Boldface genes are included among the 260 DEGs in Uganda (interaction model).