Table 7

Comparison of conservation scores between highest scoring k-mers and position weight matrices (PWM) for 20 known regulatory elements in S. cerevisiae, obtained when comparing S. cerevisiae and S. bayanus

Name

Sequence

Score

PWM consensus

Score

Bas1

AAGAGTCA

93.8*

[AG][AG]NANGAGTCA

80.9

Cbf1

CACGTGA

421.3*

[AG][AG]TCACGTG

406.5

Fkh1/2

TAAACAA

110.3

GTAAACAA[AT]

114.1*

Gcn4

TGACTCA

93.4

[AG][AG]TGA[CG]TCA

135.4*

Gcr1

TGGAAGC

82.7*

[AG]GCTTCCT CG]T

42.7

Hap4

CCAATCA

104.2*

G[AG][AG]CCAATCA

96.6

Ino4

CATGTGA

91.2*

CAT[CG]TGAAAA

61.1

Mbp1

ACGCGTC

204.1

ACGCGTNA[AG]N

210.2*

Msn2/4

AAAGGGG

140.1

A[AG]GGGG

169.7*

PAC

GCGATGAG

404.6

GCGATGAGNT

520.3*

Pdr3

CCGCGGA

76.9

[CG]NNTCCG[CT]GGAA

102.5*

Rap1

TGGGTGT

103.8

[AG]TGTN[CT]GG[AG]TG

253.2*

Reb1

CGGGTAA

Inf

[CG]CGGGTAA[CT]

Inf

Rpn4

TTTGCCACC

218.6

GGTGGCAAAA

259.4*

RRPE

AAAAATTT

509.9*

TGAAAAATTT

388.80

Ste12

TGAAACA

81.4

ANNNTGAAACA

100.0*

Sum1/Ndt80

TGACACA

135.4*

[AG][CT]G[AT]CA[CG][AT]AA[AT]

100.0

Swi4

CGCGAAA

224.1*

NNNNC[AG]CGAAAA

116.6

Ume6

TAGCCGCC

377.2

TCGGCGGC[AT]A

410.0*

Xbp1

CCTCGAG

86.7

GCCTCGA[AG]G[AC]G[AG]

141.7*

*Indicates which regulatory element representation (k-mer or weight matrix) obtained the highest conservation score. Inf corresponds to very large conservation scores, obtained when taking the negative natural logarithm of near-zero hypergeometric p-values.

Elemento and Tavazoie Genome Biology 2005 6:R18   doi:10.1186/gb-2005-6-2-r18