Normalization of microarray expression data using within-pedigree pool and its effect on linkage analysis

BMC Proceedings

Table 1 Familial correlation coefficients and maximum LOD score of non-parametric linkage analysis after RMA normalization

		Familial correlation coefficient^a
		Parent-offspring		Sibling		Grandparent-grandchild		Maximum LOD^b
Gene	Target gene loci	All arrays pool	Within pedigree pool	All arrays pool	Within-pedigree pool	All arrays pool	Within-pedigree pool	All arrays pool	Within-pedigree pool
CHI3L2	1p12	0.308	0.2689	0.1477	0.1146	0.1274	0.082	4.08	4.25
GSTM2	1p13	0.2887	0.3217	0.3284	0.3941	0.2277	0.3412	3.15	3.58
VAMP8	2p11	0.0939	0.4196	0.4304	0.7284	0.0475	0.4261	2.7	2.18
ICAP_1A	2p25	-0.2898 ^c	0.1242	0.4277	0.7435	-0.1441	0.5436	1.23	1.97
CTBP1	4p16	0.3012	0.3772	0.5581	0.639	0.2002	0.3534	0.81	0.58
PPAT	4q12	0.2055	0.2545	0.4469	0.4539	0.0778	0.1774	2.24	1.77
LOC64167	5q15	0.2927	0.3464	0.2254	0.2843	0.0483	0.1295	4.61	4.12
PSPHL	7p11	0.3932	0.5599	0.4086	0.5207	0.223	0.4089	2.51	2.54
ZP3	7q11	0.4084	0.6565	0.43	0.7211	0.2311	0.5527	4.61	3.93
IRF5	7q32	0.3462	0.384	0.2874	0.314	0.0825	0.1731	3.06	2.42
HSD17B12	11p11	0.2375	0.7565	0.3892	0.8512	0.1205	0.7026	2.06	1.96
TM7SF3	12p11	0.0618	0.5035	0.1892	0.6145	-0.1298	0.3133	1.67	1.41
RPS26	12q13	0.5907	0.6533	0.7628	0.8023	0.3606	0.453	1.58	1.57
CTSH	15q25	0.421	0.5694	0.5442	0.6546	0.322	0.5205	2.29	1.6
IL16	15q26	0.0235	0.1814	0.4244	0.5689	0.047	0.2333	2.18	1.97
CPNE1	20q11	-0.0113	0.3377	0.3958	0.73	0.0512	0.3515	1.52	0.68
CSTB	21q22	0.1592	0.3987	0.2717	0.5898	-0.0075	0.2784	2.31	1.69
DDX17	22q13	0.1687	0.2588	0.1911	0.5493	0.1911	0.2523	2.02	2.74

^aCorrelation coefficients of 18 gene expression values by familial pairs using FCOR, S.A.G.E.v5.1.0.
^bMaximum allele-sharing LOD score of nonparametric linkage analysis after RMA normalization.
^cBold text indicates negative familial correlation coefficient.

ISSN: 1753-6561