Regulatory elements of Caenorhabditis elegans ribosomal protein genes

BMC Genomics

Table 1 List of nine motifs discovered in the upstream regions of RPGs

Name	Num DME results	Num RPG instances	Num RPG seq	Upstream distribution range	Num total instances	Num total sequences	Fold enrichment	Notes
12-0	3	36	36	238-456	903	752	10.64	Co-occurrence with 12–5; Similar to CEH-14 binding site
12-5	3	27	27	253-503	884	775	8.15	Co-occurrence with 12–0; Similar to Pan binding site
12-11	3	18	18	227-464	493	383	9.75	Similar to YPR015C site
12-18	3	26	24	154-665	426	416	16.30	Similar to Zeste binding site
TGAATA	2	17	16	14-609	86	85	52.78	Novel
TTTAGG	2	39	34	71-586	1383	1283	7.53	Novel
A-rich	4	475	81	52-650	76,172	19,169	1.66	WWN₆WW
AT-rich	2	96	45	30-628	13,096	7223	1.96	WWN₆WW
Trans-splice	3	64	52	0-579	3860	3351	4.43	Half of instances overlap trans-splice acceptor sites

Column “Name” shows the motif name; “Num DME results” shows the number of DME results that were merged to form the final motif; “Num RPG instances” shows the number of sites among RPG upstream regions; “Num RPG seq” shows the number of RPG upstream regions that contain the motif; “Upstream distribution range” shows the 95% distribution range (in bp) of the motif with respect to the ATG; “Num total instances” indicates the total number of sites of the motif found in all 22,428 upstream regions by ModuleMaster [32]; “Num total sequences” indicates the number of upstream regions that contain at least one instance of each motif according to ModuleMaster; “Fold enrichment” indicates the fold enrichment of the motif in RPG upstream regions compared to all upstream regions; “Notes” indicates any other pertinent information.

ISSN: 1471-2164