Position Weight Matrix, Gibbs Sampler, and the Associated Significance Tests in Motif Characterization and Prediction

Table 1

Site-specific frequencies and position weight matrix (PWM) for 246 donor splice sites (each represented by 5 sites on the exon side and 12 sites on the intron side). The 𝜒² test is performed for each site against the expected background frequencies with A=0.3279, C=0.1915, G=0.2043, and U=0.2763. Sites that have been experimentally verified to be important are in bold.

Site	A	C	G	U	χ ^2	P	A	C	G	U
1	83	30	49	84	10.10	0.0177	0.0525	−0.6332	−0.0260	0.3143
2	103	44	46	53	10.04	0.0182	0.3613	−0.0878	−0.1162	−0.3434
3	121	36	38	51	30.01	0.0000	0.5920	−0.3739	−0.3886	−0.3981
4	122	38	33	53	32.16	0.0000	0.6038	−0.2969	−0.5893	−0.3434
5	81	40	81	44	28.33	0.0000	0.0177	−0.2238	0.6933	−0.6081
6	0	1	245	0	948.34	0.0000	−6.6464	−5.0056	2.2841	−6.6469
7	0	9	0	237	582.23	0.0000	−6.6464	−2.3190	−6.6480	1.8032
8	239	1	2	4	462.46	0.0000	1.5693	−5.0056	−4.3320	−3.8633
9	16	24	1	205	387.81	0.0000	−2.2655	−0.9496	−5.0680	1.5946
10	2	0	243	1	928.96	0.0000	−4.8476	−6.6483	2.2723	−5.3416
11	9	7	2	228	521.06	0.0000	−3.0427	−2.6612	−4.3320	1.7475
12	87	15	34	110	53.66	0.0000	0.1198	−1.6111	−0.5468	0.7006
13	84	49	30	83	11.71	0.0085	0.0696	0.0659	−0.7246	0.2971
14	111	39	33	63	19.09	0.0003	0.4684	−0.2599	−0.5893	−0.0969
15	106	38	31	71	17.24	0.0006	0.4024	−0.2969	−0.6781	0.0738
16	92	30	40	84	13.69	0.0034	0.1997	−0.6332	−0.3155	0.3143
17	80	38	36	92	14.32	0.0025	−0.0001	−0.2969	−0.4655	0.4445