Identifying breast cancer risk loci by global differential allele-specific expression (DASE) analysis in mammary epithelial transcriptome

Gao, Chuan; Devarajan, Karthik; Zhou, Yan; Slater, Carolyn M; Daly, Mary B; Chen, Xiaowei

doi:10.1186/1471-2164-13-570

Table 1 DASE Candidate Loci Identified by both SNP- and Gene-based Approaches.*

From: Identifying breast cancer risk loci by global differential allele-specific expression (DASE) analysis in mammary epithelial transcriptome

Gene_ID	SNP	SNP-based			Gene-based
		DASE	P-Value	FDR	DASE	P-Value	FDR
ACPP	rs14192	3.83	0.010497	0.0442	2.32	0.005517	0.0216
ADAMTSL3	rs2277849	3.13	0.007309	0.0359	2.25	0.014546	0.0280
AGBL1	rs10520618	3.12	0.000134	0.0279	2.37	0.000305	0.0113
C1orf94	rs6698707	3.27	0.000023	0.0016	3.27	0.000024	0.0088
CEP170P1	rs28720014	3.59	0.002355	0.0180	3.59	0.002355	0.0282
CHRAC1	rs10216653	4.31	0.007459	0.0360	4.31	0.007459	0.0425
CTAGE11P	rs477274	2.42	0.003269	0.0237	2.42	0.003269	0.0319
DMBT1	rs11523871	2.03	0.001676	0.0140	2.03	0.001676	0.0268
FAM154B	rs16973457	2.03	0.002254	0.0423	2.03	0.002254	0.0427
FLJ39061	rs10221698	4.01	0.008501	0.0379	4.01	0.008501	0.0442
FLJ42393	rs344952	2.04	0.000490	0.0449	2.25	0.000012	0.0093
GRIN3A	rs10989563	3.78	0.001589	0.0385	3.25	0.001386	0.0364
GRK4	rs1024323	2.37	0.000845	0.0532	2.71	0.000261	0.0113
	rs2960306	3.01	0.000014	0.0053	-	-	-
HCG4	rs1611213	2.19	0.003925	0.0257	2.16	0.005494	0.0098
HLA-G	rs1130363	2.52	0.001700	0.0399	3.49	0.002469	0.0170
HNRNPKP1	rs182844	2.53	0.000285	0.0071	2.53	0.000285	0.0113
HS6ST1P1	rs6423191	4.73	0.000005	0.0002	4.73	0.000005	0.0005
KHSRPP1	rs12380505	2.27	0.001212	0.0342	2.27	0.001212	0.0364
LAP3P2	rs12199346	3.55	0.000007	0.0010	3.21	0.000250	0.0113
LOC283398	rs7139313	3.74	0.000001	0.0003	2.58	0.003455	0.0178
LOC341056	rs7933723	3.70	0.002423	0.0423	3.70	0.002423	0.0428
LOC387703	rs7070947	3.61	0.000854	0.0305	3.61	0.000854	0.0355
LOC440973	rs605795	2.79	0.002160	0.0423	2.79	0.002160	0.0427
LOC442238	rs985937	4.13	0.000168	0.0114	4.13	0.000168	0.0152
LOC642590	rs9455190	3.66	0.000645	0.0486	2.50	0.000915	0.0355
LOC643618	rs732531	3.79	0.009696	0.0417	3.12	0.012274	0.0268
LOC645521	rs1976809	4.11	0.000052	0.0091	4.11	0.000052	0.0128
LOC646970	rs614805	3.38	0.008546	0.0379	3.09	0.004693	0.0207
LOC727884	rs12371762	5.21	0.002386	0.0423	4.76	0.000009	0.0002
LOC729675	rs13137565	2.36	0.003844	0.0498	2.36	0.003844	0.0522
MAGEC2	rs3765272	3.30	0.000109	0.0091	3.30	0.000109	0.0128
MMP20	rs1784423	2.32	0.001136	0.0133	2.25	0.001791	0.0268
MUC16	rs2547068	3.88	0.012106	0.0462	2.61	0.003190	0.0072
MYADML	rs11684598	5.97	0.000167	0.0114	5.97	0.000167	0.0152
NLRP1	rs11651270	2.39	0.013058	0.0479	2.87	0.000835	0.0105
NSUN4	rs17361749	2.43	0.000076	0.0091	2.43	0.000076	0.0128
OR13H1	rs17316625	3.12	0.003801	0.0498	3.12	0.003801	0.0522
OR6N1	rs857825	2.78	0.002543	0.0431	2.44	0.002721	0.0443
	rs857826	3.98	0.000430	0.0449	-	-	-
PHF2P1	rs9553323	5.08	0.000053	0.0021	4.47	0.000252	0.0048
PRDM14	rs10089937	2.07	0.002243	0.0423	2.07	0.002243	0.0427
PTCHD3	rs2484173	4.13	0.002351	0.0423	3.00	0.000427	0.0128
PTTG2	rs6811863	3.06	0.001091	0.0342	3.06	0.001091	0.0364
RPL4P4	rs13099317	4.43	0.000063	0.0011	4.43	0.000063	0.0044
RPL9P16	rs7439293	3.44	0.001159	0.0133	3.06	0.003857	0.0329
SLAMF1	rs1061217	3.42	0.000524	0.0085	3.42	0.000524	0.0137
SMARCE1P3	rs11852150	3.46	0.000020	0.0016	2.97	0.000543	0.0137
SZT2	rs2027130	2.72	0.000478	0.0085	2.39	0.003010	0.0313
TARDBPP2	rs9528094	4.81	0.000122	0.0279	2.46	0.009678	0.0454
TEX34	rs11651968	2.60	0.001264	0.0135	2.60	0.001264	0.0252
TLK2P1	rs3744516	4.00	0.004876	0.0516	4.78	0.000203	0.0046
	rs4795846	5.84	0.000008	0.0053	-	-	-
TMCC3	rs1290005	3.45	0.002658	0.0198	2.10	0.005092	0.0209
UFM1	rs2485783	3.96	0.000659	0.0082	3.96	0.000659	0.0100
UQCRFS1P2	rs13238715	3.95	0.000097	0.0091	3.02	0.003106	0.0177
USP6	rs11658877	4.80	0.001324	0.0135	4.54	0.000530	0.0086
WASF4	rs909713	4.10	0.000063	0.0091	4.07	0.000076	0.0128
WNT3A	rs752107	3.04	0.000037	0.0020	3.04	0.000037	0.0088
XIAP	rs5958343	2.46	0.005591	0.0327	2.27	0.006924	0.0423
XPNPEP2	rs3747343	2.55	0.000343	0.0073	2.55	0.000343	0.0113
ZBTB8OS	rs3753603	3.31	0.004053	0.0259	3.31	0.004053	0.0329
ZNF331	rs8110350	2.31	0.001826	0.0403	2.48	0.001014	0.0121

*: Only loci with DASE ≥ 2; P ≤ 0.01; and FDR ≤ 0.05 were included.

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ISSN: 1471-2164

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