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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]