Regulatory elements of Caenorhabditis elegans ribosomal protein genes

BMC Genomics

Table 2 Motif co-occurrence

Comparison	Upstreams containing first motif only	Upstreams containing second motif only	Upstreams containing neither motif	Intersection (upstreams containing both motifs)	P-value	Expected intersection	Intersection/ Expected intersection	Notes
12-0 and 12-5	502	525	19794	250	8.2E-178	28	9.04	Includes 12-0
A-rich and TATAAA	11261	1251	651	7908	1.4E-93	8332	0.95	Anti-occurrence
12-0 and 12-11	684	315	20004	68	1.9E-28	14	4.97	Includes 12-0
12-11 and 12-5	328	720	19968	55	3.9E-18	14	3.90
12-5 and AT-rich	411	6859	13437	364	1.3E-13	266	1.37
12-0 and TTTAGG	664	1195	19124	88	3.4E-09	46	1.92	Includes 12-0
12-0 and Trans-splice	575	3174	17145	177	3.5E-08	120	1.48	Includes 12-0
12-0 and AT-rich	423	6894	13425	329	4.9E-08	258	1.28	Includes 12-0
12-5 and Trans-splice	596	3172	17124	179	1.0E-07	123	1.45
AT-rich and Trans-splice	5951	2079	11769	1272	1.27E-06	1149	1.11
12-0 and 12-18	716	380	19939	36	1.2E-06	15	2.42	Includes 12-0
TTTAGG and Trans-splice	1017	3085	16703	266	2.2E-06	204	1.30
AT-rich and TTTAGG	6707	767	13081	516	5.2E-06	440	1.17
A-rich and AT-rich	12678	732	1170	6491	6.2E-05	6571	0.99	Anti-occurrence
12-5 and TTTAGG	701	1209	19087	74	1.2E-04	47	1.57
12-18 and 12-5	385	744	19911	31	1.9E-04	15	2.03

Out of all 22,428 upstream regions, 21,071 contained at least one instance of one motif or the same-strand TATAAA sequence. For each pair of motifs (including TATAAA), the upstream regions were divided into four categories: Upstream regions that contained the first motif but not the second, upstream regions that contained the second motif but not the first, upstream regions that contained neither of the two motifs, and upstream regions that contained both motifs (the intersection). We calculated the probability of this distribution by the Fisher Exact Test. We also calculated the expected intersection, based on the individual frequency of each motif, and then calculated the ratio of the actual intersection to the expected intersection to show whether the motif pairs co-occurred more or less frequently than expected. Shown are those motif pairs whose p-values of co-occurrence were more significant than a Bonferroni-adjusted threshold of 0.0002 (0.01/45 comparisons). Motif pairs that include motif 12–0 and motif pairs that co-occurred in fewer upstream regions than expected are indicated in column “Notes”.

ISSN: 1471-2164