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Table 2 Evolution of motifs with known consensus, but binding sites identified by MEME

From: Position specific variation in the rate of evolution in transcription factor binding sites

Cluster

Factor

Consensus identified by MEME

Motif subs.

Bg subs.

Corr.

p-value

Protein folding +

Hsf1p

TTTTC TAGAA AGTTC

0.14

0.68

-0.42

0.060

Glycolysis +

Gcr1p

AAATAGAGGAAG CCCA

0.23

0.63

-0.80

<0.001 **

Nitrogen +

Gln3p/ Dal80p

TCTTAT CA

0.39

0.74

-0.78

0.010 *

Gluco-neogenesis +

Sip4p (?) CSRE

CC GTTTGTCCG

0.33

0.57

-0.84

<0.001 **

G1 phase +

Mbp1p Swi6

TTACGCGT TTT

0.22

0.64

-0.67

0.011 *

Respiration +

Hap2/3/4p

TGATTGG TCCA

0.20

0.67

-0.53

0.048 *

Methionine +

Cbf1p

ATGTCACGTG

0.13

0.75

-0.49

0.078

Proteasome +

Rpn4p

ATTTTGCCACC G

0.20

0.73

-0.75

0.002 *

M/G1 transition +

Swi5p/ Ace2p

AACCAGC A

0.26

0.61

-0.57

0.074

Repressed in Stress ++

(?) PAC

ATGCGATGAG CTGAG

0.24

0.71

-0.69

0.006 *

leu/ilv bio-synthesis++

Leu3p

GCCG TTTCCGG

0.31

0.70

-0.54

0.044 *

Phosphate +++

Pho4p

CCCACGTG CG

0.29

0.65

-0.74

0.005 *

119 positions in all computationally identified motifs

-0.60

4e-14 **

  1. Here binding sites are identified by running the MEME program [3] on genes that clustered with targets in micro-array gene expression data. Expected consensus sequences (from [20, 40] or [7]) are underlined. 'Motif subs.' and 'bg subs.' are the substitutions per site in the binding sites and the promoters in which they are found respectively. 'Corr.' and 'p-value' are the Spearman's rank correlation coefficient and the associated p-value between the rate of evolution at each position and the information content at each position. * Indicates significance at a per factor error rate of < 0.05. ** Indicates significance after Bonferoni correction for a global error rate < 0.05, assuming 50 tests were done in total. (?) indicates uncertainty as to the identity of the binding protein. + indicates clusters taken from hierarchical clustering [40] of yeast data from the Stanford Microarray database [42], ++ indicates clusters taken from hierarchical clustering of 300 genetic perturbations [43] and +++ indicates clusters taken from hierarchical clustering of 64 control experiments [43]