Computational selection and prioritization of candidate genes for Fetal Alcohol Syndrome

BMC Genomics

Table 6 Pairs of promoter elements found to be enriched in the target promoter set relative to the background promoter set

Pairs of promoter elements	ORI	TAR (%)	BCG (%)	Probability of finding PE in target set	Probability of finding PE in background set	TAR (n)	BCG (n)	TAR Total	BCG Total	P-value
-1 MZF1/+1 E2F	17.1036	6.62	1.47	0.00007	0.00002	36	151	544	10255	0.000003
-1 LEF1/-1 Pax-4	14.6726	6.62	1.77	0.00007	0.00002	36	182	544	10255	0.000254
-1 C/EBP/+1 VDR	10.1454	6.43	1.85	0.00006	0.00002	35	190	544	10255	0.002385
+1 C/EBP/+1 VDR	9.1022	6.99	2.42	0.00009	0.00003	38	248	544	10255	0.041880
-1 MAZ/-1 VDR	9.0220	9.19	2.89	0.00015	0.00005	50	296	544	10255	0.000012
-1 MZF1/-1 MZF1	8.4560	5.51	1.6	0.00007	0.00003	30	164	544	10255	0.039710
-1 ETF/-1 VDR	7.6725	7.54	2.68	0.00011	0.00004	41	275	544	10255	0.023710
-1 AP-2/-1 ETF	6.8853	12.87	5.11	0.00023	0.00009	70	524	544	10255	0.000015
-1 MAZ/+1 Sp1	6.4534	9.56	2.63	0.00012	0.00007	52	270	544	10255	0.000000
-1 Spz1/-1 Spz1	6.0515	14.34	5.57	0.00021	0.00009	78	571	544	10255	<0.00001
-1 VDR/-1 Spz1	5.4345	14.34	6.54	0.00024	0.00010	78	671	544	10255	0.000429
-1 ETF/-1 E2F	5.4001	11.76	5.22	0.00020	0.00009	64	535	544	10255	0.007227
-1 Spz1/-1 VDR	5.2463	13.6	6.58	0.00025	0.00010	74	675	544	10255	0.013100
-1 VDR/+1 ZF5	4.4308	14.15	6.59	0.00018	0.00009	77	676	544	10255	0.001322

The criteria for selecting pairs of PE as enriched was that it has to appear in at least 5% of the target promoter sequences and to have over-representation index (ORI) of at least 2. PE that appear in statistically significant proportion in the target set are denoted by + in the ORI column.

ISSN: 1471-2164