GentrepidV2.0: a web server for candidate disease gene prediction

BMC Bioinformatics

Table 1 Comparison of reported genes and candidate disease genes predicted by Gentrepid using the gene search space from the adjacent mapping

Reported SNP	Reported gene(s) by study	Predicted candidate gene(s)	Method	Common property used in prediction	Seed gene	Score	Relative rank
rs419076	MDS1, EVI1	EVI1	CMP-ab	zf-C2H2	-	S = 5.17	3
rs13107325	SLC39A8	SLC39A8	CMP-ab	Zip	-	S = 150.96*	1
rs13107325	SLC39A8	NFKB1	CPS-s	Corticosteroids & cardioprotection	NOS3	P = 0.09	1
rs13139571	GUCY1A3,	GUCY1A3,	CPS-ab	Purine metabolism	-	P = 0.23	7
	GUCY1B3	GUCY1B3	CPS-ab	Purine metabolism	-	P = 0.23	7
			CPS-s	Long-term depression	NOS2A,	P = 0.39	7
			CPS-s	Long-term depression	NOS3	P = 0.39	7
rs4373814	CACNB2	SLC39A12	CMP-ab	Zip	-	S = 150.96*	1
rs932764	PLCE1	PLCE1	CPS-ab	Calcium signaling pathway	-	P = 0.31	11
			CPS-s	Calcium signaling pathway	AGTR1,	P = 0.31	5
					NOS2A,
					NOS3
rs7129220	ADM	AMPD3	CPS-ab	Purine metabolism	-	P = 0.23	9
rs2521501	FURIN, FES	FES	CMP-ab	Pkinase_Tyr	-	S = 13.97	2
rs17608766	GOSR2	WNT9B	CPS-ab	Basal cell carcinoma	-	P = 0.05*	3
rs6015450	GNAS, EDN3, ZNF831, MRPS16P	C20orf174	CMP-ab	zf-C2H2	-	S = 5.17	3
rs3774372	ULK4	CTNNB1	CPS-ab	Cell to Cell Adhesion Signaling	-	P = 0.01*	1
rs1458038	FGF5	FGF5	CPS-ab	MAPK signaling pathway	-	P = 0.08	5
rs1458038	FGF5	PRDM8	CMP-ab	zf-C2H2	-	S = 5.17	3
rs1813353	CACNB2	CACNB2	CPS-ab	MAPK signaling pathway	-	P = 0.08	5
rs17249754	ATP2B1	ATP2B1	CPS-ab	Calcium signaling pathway	-	P = 0.31	11
			CPS-s	Calcium signaling pathway	AGTR1,	P = 0.31	5
					NOS2A,
					NOS3
rs1378942	CYP1A2, CSK	CYP1A2	CMP-s	p450	CYP3A5	S = 0.15	1
		CSK	CPS-s	PPIN	ACSM3,	-	-
		CSK	CPS-s	PPIN	ADD1	-	-
rs12940887	ZNF652	ZNF652	CMP-ab	zf-C2H2	-	S = 5.17	3

All predictions are reported. CMP/CPS s: seeded. ab :ab initio. Score (S) or p-value (P) reported for genes predicted. Significant scores or p-values are marked with an *. A dash (−) indicates no prediction. Relative rank is the rank of the gene in the method used. For PPIN, no rank has been assigned.

ISSN: 1471-2105