Impact of polymorphisms in microRNA biogenesis genes on colon cancer risk and microRNA expression levels: a population-based, case-control study

Mullany, Lila E.; Herrick, Jennifer S.; Wolff, Roger K.; Buas, Matthew F.; Slattery, Martha L.

doi:10.1186/s12920-016-0181-x

Table 3 SNPs associated with mRNA expression in normal mucosa, carcinoma tissue and differential across genotypes

From: Impact of polymorphisms in microRNA biogenesis genes on colon cancer risk and microRNA expression levels: a population-based, case-control study

			Tumor		P-values (carcinoma)		Normal		P-values (normal)		P-values (difference)		VEP prediction
Gene	SNP	Model	N	Mean^c mRNA expression	Raw	FDR	N	Mean mRNA expression	Raw	FDR	Raw	FDR	VEP prediction
ADAR	rs3766925	TT	38	831.03	0.047	0.749	36	426.06					Modifier
		TA/AA	33	518.97			31	306.42
AGO2	rs7460^b	AA	19	284.79	0.027	0.316	18	113.50	0.021	0.267			Modifier
		AT/TT	52	160.38			49	70.65
AGO2	rs1060832	CC/CT	70	191.79			66	83.06			0.050	0.403	Modifier
		TT	1	326.00			1	23.00
AGO2	rs13276958	TT/TC	56	172.75			51	88.39			0.022	0.403	Modifier
		CC	15	271.80			16	62.31
AGO2	rs2176397	CC/CT	66	174.39	0.043	0.316	60	78.37					Modifier
		TT	5	448.20			7	114.71
AGO2	rs2271735	CC/CA	66	205.17	0.009	0.223	61	88.84	0.019	0.267			Modifier
		AA	5	42.00			6	14.33
AGO2	rs2292775	GG/GA	70	191.79			66	83.06			0.049	0.403	Modifier
		AA	1	326.00			1	23.00
AGO2	rs2292780	CC/CT	70	191.79			66	83.06			0.048	0.403	Modifier
		TT	1	326.00			1	23.00
AGO2	rs2293939	GG/GA	65	204.00	0.039	0.316	60	85.65					Low
		AA	6	81.83			7	52.29
AGO2	rs2944760	TT/TG	67	190.13			63	84.56			0.038	0.403	Modifier
		GG	4	253.00			4	44.50
AGO2	rs2944761	GG	18	272.83	0.039	0.316	17	104.76	0.049	0.365			Modifier
		GA/AA	53	166.79			50	74.48
AGO2	rs2977490	GG	21	161.81	0.034^a	0.316	17	131.29	0.016	0.267			Modifier
		GA/AA	50	207.06			50	65.46
AGO2	rs10087629	GG	22	300.91	0.005	0.223	21	115.14	0.009	0.267			Modifier
		GA/AA	49	145.53			46	67.11
BMP2	rs15705	AA/AC	68	26.35	0.039	0.308	64	63.50					Modifier
		CC	3	43.33			3	70.33
BMP2	rs235768	TT/TA	63	28.84			58	71.78	0.003	0.035	0.049	0.535	Moderate
		AA	8	13.13			9	12.44
DCP1B	rs2240610	GG/GA	52	29.46			51	12.47	0.009	0.127			Modifier
		AA	19	31.79			16	29.00
DCP1B	rs6489338	GG/GA	54	28.48			53	12.30	0.004	0.114			Modifier
		AA	17	35.18			14	32.00
DDX5	rs1140409	AA	68	710.12	0.044	0.292	64	562.19					Moderate
		AC/CC	3	212.67			3	88.33
DHX16	rs3130000	GG	60	80.68			55	63.58			0.045	0.696	Modifier
		GA/AA	11	64.36			12	74.08
DICER1	rs4513027	AA/AG	65	348.18			61	286.57			0.047	0.554	Modifier
		GG	6	290.00			6	64.50
DROSHA	rs573010	CC	38	230.03			37	87.57			0.038	0.769	Modifier
		CA/AA	33	172.42			30	108.30
DROSHA	rs673019	AA	61	221.62	0.015	0.361	60	102.13					Modifier
		AG/GG	10	91.20			7	51.57
DROSHA	rs2330696	GG	46	224.61			40	88.18			0.008	0.470	Modifier
		GA/AA	25	163.96			27	109.70
DROSHA	rs3792830	AA/AG	70	200.31	0.028	0.361	66	95.74					Modifier
		GG	1	409.00			1	170.00
DROSHA	rs3805525	TT/TC	61	207.46			57	87.16	0.050	0.569	0.026	0.769	Modifier
		CC	10	177.60			10	152.10
DROSHA	rs6878195	TT	23	174.43			20	56.10	0.020	0.569			Modifier
		TC/CC	48	217.06			47	114.19
DROSHA	rs7719666	CC/CT	49	214.47			48	112.17	0.034	0.569			Modifier
		TT	22	178.27			19	58.16
DROSHA	rs10052174	AA/AG	70	200.31	0.030	0.361	66	95.74					Modifier
		GG	1	409.00			1	170.00
DROSHA	rs10067066	TT/TC	70	200.31	0.028	0.361	66	95.74					Modifier
		CC	1	409.00			1	170.00
DROSHA	rs13183642	GG	44	169.70			39	79.23	0.030	0.569			Modifier
		GT/TT	27	257.93			28	121.39
DROSHA	rs16901165	GG/GA	70	200.31	0.029	0.361	66	95.74					Modifier
		AA	1	409.00			1	170.00
FAM57A	rs2740351	AA/AG	58	42.79			54	20.30	0.006	0.089			Modifier
		GG	13	24.92			13	4.54
FKBP5	rs755658	CC	59	122.02			56	179.54	0.042	0.232			Modifier
		CT/TT	12	82.50			11	69.09
GEMIN4	rs7813	AA/AG	58	59.29			54	32.72	0.023	0.113			Modifier
		GG	13	28.62			13	8.69
GEMIN4	rs2740348	CC	51	64.31			47	35.26	0.013	0.089			Moderate
		CG/GG	20	26.55			20	11.15
GEMIN4	rs2740349	TT	51	64.31	0.005	0.047	47	35.26	0.012	0.089			Moderate
		TC/CC	20	26.55			20	11.15
MAPK1	rs743409	GG/GA	60	280.25			56	201.55			0.032	0.979	Modifier
		AA	11	341.64			11	126.00
MAPK14	rs8510	CC	60	246.67			56	147.52	0.016	0.157			Modifier
		CT/TT	11	193.64			11	62.91
PRKRA	rs2059691^b	GG	33	48.67	0.044^a	0.428	30	15.37	0.000	0.003			Modifier
		GA/AA	38	89.16			37	51.24
RBBP6	rs2033214	TT	58	200.36			56	130.27	0.038	0.418			Modifier
		TG/GG	13	119.23			11	51.00
SKIV2L	rs449643	CC	52	73.13	0.016	0.458	50	51.50					Moderate
		CT/TT	19	136.58			17	95.35
TARBP2	rs34649330	CC/CT	69	22.33	0.037	0.685	65	10.69			0.024	0.640	Modifier
		TT	2	51.50			2	10.00
TNRC6A	rs1030211	AA	56	266.98	0.044	0.299	55	228.71					Modifier
		AG/GG	15	189.33			12	138.83
TNRC6A	rs4788430	GG	41	298.59	0.010	0.212	39	252.33					Modifier
		GA/AA	30	184.97			28	157.29
TNRC6A	rs6497755	AA	23	316.39	0.030	0.299	22	303.50	0.009	0.194			Modifier
		AC/CC	48	219.04			45	168.18
XPO5	rs11077	TT/TG	57	178.12			55	70.96	0.017	0.157			Modifier
		GG	14	328.86			12	134.83
XPO5	rs1106841	AA/AC	59	183.85			57	73.46	0.036	0.232			Low
		CC	12	325.83			10	133.40
XPO5	rs2257082	GG/GA	66	208.95			62	75.56	0.012	0.157			Low
		AA	5	193.20			5	167.20

^a This p-value is for the recessive model
^b This mRNA was significantly differentially expressed across genotypes using both the recessive and dominant models
^c Means are displayed in count data (rather than RPKMs)

Back to article page

ISSN: 1755-8794

Contact us

Submission enquiries: bmcmedicalgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com

BMC Medical Genomics

Contact us