Table 3

Motifs identified by MEME that do not correspond to the expected consensus sequences for the transcription factors thought to be regulating the cluster.

Cluster

Factor (expected)

Consensus identified by MEME

Motif subs.

Bg. subs.

Corr.

p-val

TRX2 +

Yap1p

AAAAAGAGGAAAAAA

0.80

0.78

-0.21

0.23

CTT1 +

Msn2/4p

GAAAAAAAAAAAAAA

0.51

0.67

0.13

0.67

Transport ++

Pdr1/3p

AAAGAGAGAAAAAAA

0.57

0.69

0.20

0.76

Ergosterol bio-synthesis++

Upc2p/ Ecm22p

ATCTTTTTTTTTTTT

0.81

0.55

0.06

0.58

60 positions in background sequence

0.08

0.73

These motifs do not show the characteristic correlation with rate of substitution or the substantial decrease in substitution rate observed for the computationally identified motifs with the expected consensus. + indicates clusters taken from hierarchical clustering of yeast data from the Stanford Microarray database [42], ++ indicates clusters taken from hierarchical clustering of 300 genetic perturbations [43].

Moses et al. BMC Evolutionary Biology 2003 3:19   doi:10.1186/1471-2148-3-19