Cis-regulatory variations: A study of SNPs around genes showing cis-linkage in segregating mouse populations

BMC Genomics

Table 2 SNP density in the promoter or non-coding regions of CEGs and non-CEGs

Gene Set	Region	Number of CEGs	Number of Non-CEGs	SNP Density (Normalized by total non-coding or promoter length)			SNP Density (Normalized by Conserved or Non-Cons region length)
				Mean SNP Density CEGs	Mean SNP Density Non-CEGs	WRST p-value	Mean SNP Density CEGs	Mean SNP Density Non-CEGs	WRST p-value
Full Combined Set	NCR	1769	1745	0.630	0.463	< E-12	NA	NA	NA
	Prom 2 Kb	863	706	1.291	1.172	0.008	NA	NA	NA
	Prom 5 Kb	1220	1040	0.789	0.685	2.70E-06	NA	NA	NA
Genes with No	NCR	987	1051	0.546	0.352	< E-12	NA	NA	NA
SNPs in Conserved		Prom 2 Kb	741	592	1.243	1.106	0.009	NA	NA
Regions (subset 1)	Prom 5 Kb	1024	848	0.731	0.620	1.50E-06	NA	NA	NA
Genes having SNPs	All NCR			0.736	0.630	5.00E-10	NA	NA	NA
in Conserved	Non Cons NCR	782	694	0.657	0.554	9.00E-09	0.732	0.620	1.00E-08
Regions (subset 2)	Cons NCR			0.091	0.101	0.050	1.359	1.193	2.71E-06
	All Prom 2 Kb			1.581	1.513	0.172	NA	NA	NA
	Non Cons 2 Kb	122	114	1.376	1.415	0.498	1.886	2.169	0.482
	Cos Prom 2 Kb			0.758	0.706	0.278	5.227	5.721	0.026
	All Prom 5 Kb			1.091	0.967	0.036	NA	NA	NA
	Non Cons 5 Kb	196	192	0.910	0.822	0.119	1.139	1.025	0.174
	Cons Prom 5 Kb			0.357	0.317	0.036	3.763	3.276	0.001

"SNP density (Normalized by total non-coding or promoter length)" = 1000*(total number of SNPs in non-coding or promoter sequence)/(total non-coding or promoter length). "SNP density (Normalized by Conserved or Non-Cons region length)" = 1000*(the number of SNPs in conserved or non-conserved regions)/(total length of the conserved or non-conserved sequence in promoters or non-coding regions). "Mean SNP density" gives the average SNP-density over all the genes in a particular set. The means are only given for reference, and have not been used for calculation of p-values (which were done using a non-parametric method). p-values of significance with the Wilcoxon rank sum test (WRST) are given. H₀ = CEGs and non-CEGs have equal SNP density, H_A = CEGs have higher SNP density compared to non-CEGs. p-values less than 0.01 are in bold.

ISSN: 1471-2164