Association between polymorphisms of immune response genes and early childhood caries — systematic review, gene-based, gene cluster, and meta-analysis

Aruna, P.; Patil, Sneha S.; Muthu, M. S.; Vettriselvi, V.; Arockiam, Selva; Kirubakaran, R.; Sivakumar, N.

doi:10.1186/s43141-023-00566-x

Journal of Genetic Engineering and Biotechnology

Table 2 Gene-based analysis of immune response genes

From: Association between polymorphisms of immune response genes and early childhood caries — systematic review, gene-based, gene cluster, and meta-analysis

Symbol	Chromosome	Start position	Group	SNP	Position	Gene Feature	Meta-P	Fischers	Simes	GATES^a	ECS^b	Inverse	Weighted TPM^c	Unweighted TPM	ARTP^d
TRAV4	14	21677306	Protein-coding gene	rs1997533	21729284	Intronic	0.0005	0.0026688	0.002	0.042	0.042	0.007375	0.00218	0.001962	0.001744
				rs8011979	21733619	Intronic	0.009
				rs7150049	21733607	Intronic	0.01
				rs1997532	21729203	Intronic	0.01
TNF-α	6	31554976	Protein-coding gene	rs1800629	31557394	Exonic	0.023	0.026688	0.023	0.0805	0.0805	0.023	0.025185	0.0226665	0.015111
		31654731		rs1800629	31651559	Upstream	0.023
		31644460		rs1800629	31651559	Upstream	0.023
		31606804		rs1800629	31614702	Intronic	0.023
		31557048		rs1800629	31562660	Upstream	0.023
				rs1800629	31565480	Upstream	0.023
				rs1800629	31557394	Exonic	0.023
ALOX15	17	4637803	Protein-coding gene	rs2619112	4632090	Upstream	0.04	0.06672	0.05	0.116666667	0.116666667	0.045	0.05475	0.049275	0.0438
ALOX15	17	4637803	Protein-coding gene	rs7217186	4636097	Intronic	0.05	0.06672	0.05	0.116666667	0.116666667	0.045	0.05475	0.049275	0.0438
MBL2 -	10 -	52750647 -	Protein-coding gene	rs7096206	52771925	Intronic	0.023	0.092046	0.069	0.1449	0.1449	0.1365	0.075831	0.0682479	0.0606648
MBL2 -	10 -	52750647 -	Protein-coding gene	rs1800450	52771475	Intronic	0.25	0.092046	0.069	0.1449	0.1449	0.1365	0.075831	0.0682479	0.0606648
DEFB1	8	6873390	Protein-coding gene	rs1800972	6877901	Upstream	0.02	0.160128	0.12	0.200307692	0.200307692	0.2693333	0.13164	0.118476	0.105312
				rs1799946	6877871	Upstream	0.074
				rs1799946	6877909	Upstream	0.314
				rs11362	6877839	Upstream	0.314
				rs1800972	6877863	Upstream	0.432
				rs11362	6877877	Upstream	0.462
LTF	3	46458006	Noncoding RNA	rs4547741	46458968	ncRNA	0.036	0.1894848	0.142	0.208631956	0.208631956	0.6392	0.155774	0.1401966	0.1090418
				rs1126478	46459723	ncRNA	0.062
				rs17078878	46459610	ncRNA	0.382
		46449105	Protein-coding gene	rs743658	46446997	Upstream	0.08
		46449105	Protein-coding gene	rs2269436	46445762	Upstream	0.396
LPO	17	58254688	Protein-coding gene	rs7209537	58250853	Downstream	0.093	0.38654232	0.289675	0.337295231	0.337295231	0.09974	0.317773475	0.285996128	0.25421878
		58254688	Protein-coding gene	rs3744093	58415439	Intronic	0.1102
		58227333	Protein-coding gene	rs7209537	58250853	Downstream	0.093
				rs8178329	58249160	ncRNA	0.1183
				rs8178281	58239832	Downstream	0.2874
HLA DRB1	6 6	32358286	Noncoding RNA	rs3763305	32359153	Downstream	0.199	0.3796368	0.2845	0.338745098	0.338745098	0.256	0.3120965	0.28088685	0.21846755
		32361115	Protein-coding gene	rs3763305	32359153	Downstream	0.199							0.28088685	0.21846755
		32361115	Protein-coding gene	rs3763305	32377195	Upstream	0.37							0.001962	0.001744

^aGene-based Association Test using extended Simes procedure
^bExtended chi-square
^cTruncated product method
^dAdaptive Rank truncated Product

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