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Table 1 Performance of the hill climbing algorithm on well-characterized S. cerevisiae regulons. The reported binding sites were each run through the hill climbing algorithm to determine the algorithm's ability to generate a representative consensus motif given only one instantiation. Abbreviations are as follows: |B|-the number of genes in the regulon; HC(b)-the consensus motif reported by HC(·) that had the highest Φ score; ΔSig-the maximum change in Sig score due to HC for any binding site; Φ b-the maximum Φ score for any one binding site; Φ HC-the Φ score after HC is run on the known binding sites.

From: Bounded search for de novo identification of degenerate cis-regulatory elements

Regulon |B| HC(b) ΔSig Φ b Φ HC
BAS1 13 gagtca 17.80 0.36 0.36
CPF1 3 cwcgtgrm 17.26 0.61 0.55
CSRE 6 tcmwttcayccg 28.33 0.27 0.29
GATA 5 gatwas 40.66 0.73 0.56
GCN4 20 bagtcab 26.10 0.29 0.44
GCR1 9 ctyhc 12.59 0.43 0.18
GLN3 3 ytaatctaatc 10.28 0.63 0.64
HAP2 5 gttggttggtgga 13.37 0.37 0.23
MATA1 3 sactaattaggaaa 10.00 0.33 0.36
MATA2 12 brdgtaadt 29.17 0.21 0.48
MCM1 43 chnwttmggdaa 53.31 0.05 0.29
MCB 4 wcgcg 40.46 0.62 0.78
MIG1 13 ccccrbwww 19.43 0.21 0.38
PDR3 10 hyccrcggr 138.96 0.50 0.71
PHO2 6 gtaaattagttaatt 0.00 0.40 0.21
PHO4 12 cacgtggracta 8.41 0.13 0.14
RAP1 18 acacccagacmkc 12.98 0.09 0.15
REB1 20 bvywacccs 25.01 0.36 0.47
ROX1 8 ycyattgttctc 14.86 0.13 0.38
RPA 3 tctcggcggtta 0.00 0.34 0.34
SCB 8 cdcgawa 37.79 0.58 0.72
SFF 4 aggtmaacaa 5.85 0.25 0.50
STE12 6 atgmaac 24.74 0.48 0.53
TBP 20 yatava 18.44 0.44 0.20
UASCAR 4 ttgccmttmgc 16.63 0.25 0.40
UASH 21 gwgtagtgaca 12.12 0.05 0.05
UASPHR 23 cgtggatgaaac 6.44 0.04 0.04
UIS 5 aaaatagcgcctc 0.00 0.22 0.20
URS1H 12 wdwtwgccsccvw 61.10 0.15 0.65
Average 11   24.21 0.33 0.39