Features generated for computational splice-site prediction correspond to functional elements

BMC Bioinformatics

Table 5 FGA-generated feature set show significant overlap with ESE and ESS regulator signal sets.

*FGAset*	*size*	*AstESR (285)*		*RescueESE (238)*		*ChPESE (1701)*		*FasESS (176)*		*ChPESS (924)*
		*Overlap, P-value*		*Overlap, P-value*		*Overlap, P-value*		*Overlap, P-value*		*Overlap, P-value*
A-3mer3 [1,80]	313	34	0.00514	24	0.09415	175	2.09e-06	10	0.877	73	0.5407
A-3mer3 [1,80]+	177	28	0.00003	24	0.00007	130	1.42e-18	1	0.999	8	*
A-3mer3 [1,80]-	136	6	0.92089	0	*	43	0.9939	9	0.129	59	3.19e-08
A-4mer2 [1,80]	317	35	0.00347	26	0.04319	177	1.96e-06	10	0.887	72	0.6423
A-4mer2 [1,80]+	179	29	0.00001	25	0.00003	129	2.74e-17	1	0.999	9	*
A-4mer2 [1,80]-	138	6	0.92714	1	0.99999	46	0.9819	9	0.137	57	4.22e-07
A-5mer1 [1,80]	342	35	0.01147	27	0.05920	278	1.06e-08	12	0.812	70	0.9300
A-5mer1 [1,80]+	187	29	0.00003	25	0.00006	134	1.40e-17	3	0.999	9	*
A-5mer1 [1,80]-	155	6	0.96496	2	0.99915	59	0.8352	9	0.221	54	0.000257
A-6mer [1,80]	465	54	0.00006	27	0.53401	278	1.06e-08	17	0.799	91	0.9993
A-6mer [1,80]+	263	38	0.00001	25	0.00899	165	6.61e-13	7	0.943	19	*
A-6mer [1,80]-	202	16	0.32994	2	0.99984	76	0.8907	10	0.368	64	0.001374
D-5mer1 [-80,-1]	64	10	0.01195	32	1.32e-23	60	5.59e-19	1	0.941	4	0.9999
D-5mer1 [-80,-1]+	56	9	0.01403	30	2.47e-23	52	4.27e-16	0	*	4	0.9995
D-6mer [-80,-1]	1052	126	1.44e-12	112	1.81e-13	613	3.73e-37	26	0.999	183	0.9999
D-6mer [-80,-1]+	701	93	2.28e-11	109	6.16e-28	482	1.02e-57	6	0.999	63	*
D-6mer [-80,-1]-	271	20	0.42504	1	0.99999	90	0.9985	19	0.022	106	1.54e-10

* p-value is very close to 1.
The number of shared features between the FGA generated sets of hexamers and the exon regulator hexamer sets and the p-value stating the probability of having this overlap or a greater overlap by chance. We highlight the highly statistically significant probabilities. The set D -3mer 3 [-80,-1] did not contain position specific hexamers and the set D -4mer 2 [-80,-1] contained only 3 position specific hexamers, two of which overlapped with RescueESE set.

ISSN: 1471-2105