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Table 2 Known regulatory elements obtained when applying FastCompare to C. elegans and C. briggsae

From: Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach

Sequence Rank DATG WATG Orientation U/C Experiment TRANSFAC Comments
TGATAAG 5 746 [0;600] ← (p < 10-6) 1.67 103(56/47) GATA-1, GATA-2 Known GATA factor
AATCGAT 6 865.5 [0;1900] - 1.00 14(2/12) CDP, Clox Similar to DRE, embryonic development (p < 10-8)
TGACTCAT 8 708 - → (p < 10-4) 1.40 - AP-1, GCN4, NF-E2 Known AP-1 site
GTGTTTGC 9 383.5 [0;800] - 2.44 - - Known forkhead-related activator 4
CACGTGG 16 935 - - 0.73 12(9/3) Myc/Max, PHO4, USF Known Myc-Max site in Drosophila
AAGGTCA 22 882 [0;1400] - 1.52 35(16/19) ER, HNF-4 Known HRE
TGACGTC 32 858 [0;1700] - 0.94 1(1/0) CREB, ATF Known CREB site
TGTCATCA 42 879 - - 0.80 - Skn-1 Known SKN-1 site
CAGCTGG 56 1093 [100;2000] - 0.67 5(2/3) AP-4, HEN-1 Known AP-4 and MyoD/CeMyoD site
AGAGAGA 57 893 - → (p < 10-90) 1.43 4(2/2) - Known GAGA-factor site
GTAAACA 79 818 [0;400] - 2.69 28(28/0) Freac, SRY Known DAF-16 site
CCCGCCC 88 535 [0;1400] - 2.48 1(0/1) Sp1, GC box Known Sp1 site
ATCAATCA 100 911 - - 0.93 1(1/0) Pbx-1 Known Pbx-1 site
CAGGTGA 111 845 [0;200] - 2.25 - Lmo2, RAV1 Known Snail site in Drosophila
TTCGCGC 148 651.5 [0;1200] - 1.7 16(7/9) E2F Known E2F site, embryonic development (p < 10-6)
  1. For each known regulatory element, we show the best k-mer, its rank within the set of 437 highest scoring k-mers, the median distance to ATG (for occurrences upstream of genes within the conserved set), the optimal window, the orientation bias, the corrected ratio of upstream/coding bias, the total (up-regulated/down-regulated) number of microarray conditions in which the k-mer was found (see Materials and methods), TRANSFAC matches, and the best GO enrichment.
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