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.

Sleumer et al.

Sleumer et al. BMC Genomics 2012 13:433   doi:10.1186/1471-2164-13-433

Open Data