Identification of functional tumor necrosis factor-alpha promoter variants associated with Helicobacter pylori infection in the Sudanese population: Computational approach

Table 5 Summary of the in silico predicted transcription factor binding sites for tumor necrosis factor-alpha (-146 to +10) region

TranscriptionFactor	Position1		SNP in binding site	Software
	Start	End		AliBaba2.1	Alggen Promo		Tfsitescan	TF-Binding		GPMiner
Elk-1	-145	-130				X2			X
Sp1	-138	-126		X			X
AP-2	-129	-118				X			X
Ets-1	-118	-111					X
PEA3/ Ets-1	-118	-110					X
T3R_TRE1	-115	-108				X	X		X
TNF-alpha-CRE	-112	92					X		X
C/EBP-beta	-100	-74	rs41297589 [-76]3				X		X
NF-kappaB	-99	-86					X		X
AP-1	-67	-57					X
NF-kappaB	-55	-46	rs765073823 [-48]rs537401710 [-47]	X
Sp1	-54	-41	rs765073823 [-48]rs537401710 [-47]	X		X	X
Sp1	-48	-39	rs765073823 [-48]rs537401710 [-47]	X		X	X
GATA	-40	-30	rs539666421 [-38]	X		X			X
AP-2	-38	-27	rs539666421 [-38]	X			X		X
TBP	-29	-20		X					X	X

¹Position is relative to the tumor necrosis factor-alpha transcription start site.

²X means the transcription factor is predicted by the software that is marked with X.

³Observed in this study. SNP: Single nucleotide polymorphism.