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Table 1 Identified known motifs in the promoters of 645 yeast cell-cycle genes

From: A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements

Transcription factors

Known motifs

WordSpy

Z-score

Z g -score

G-score

Rank

MobyDick

RSA

Weeder

Ace2, Swi5

RRCCAGCR [19]

CCAGC(-)

5.4

5.2

0.0363

8/3/29

ACCCGGCTGG

N/A

N/A

  

GCCAGC(+)

5.3

2.6

0.0551

36/4/58

   
  

AGCCAGC(+)

4.6

2.5

0.0688

75/13/199

   
  

CCAGCAAA(-)

4.3

3.5

0.113

107/51/867

   
  

CCAGCAAG(-)

3.9

2.9

0.0976

185/67/867

   
  

GCCAGCAA(-)

3.9

3.4

0.1872

124/12/867

   
  

AGCCAGCA(+)

5.7

2.7

0.0929

189/73/867

   
 

ACCAGC [59, 60]

AACCAGCA(+)

3.8

2.6

0.1983

239/8/867

   

Swi6, Mbp1

ACGCGT [19, 60]

AACGCGT(+)

13.7

11.3

0.1816

1/1/199

AACGCGT

AAACGCGT

ACGCGT

  

GACGCGTC(+)

9.3

4.9

0.2106

41/4/867

ACGCGTC

ACGCGTAA

ACGCGTAA

  

AAACGCGT(+)

14.6

10.2

0.2093

3/5/867

 

AACGCGTC

CGACGCGT

  

AACGCGTC(*)

10.8

8.9

0.2003

9/7/867

 

ACGCGTCA

GACGCGTA

  

ACGCGTAA(*)

9.6

9.0

0.1341

7/36/867

 

ACGCGTCG

AAACGCGT

  

ACGCGTCA(*)

8.9

7.3

0.1291

15/41/867

 

AACGCGTT

GACGCGTG

  

CAACGCGT(+)

6.3

4.0

0.1014

73/59/867

 

AACGCGTA

 

Swi4, Swi6

CACGAAA [19, 60]

CACGAAA(*)

4.6

5.7

0.0623

10/17/199

CGCGAAA

ACGCGAAA

ACGCGAAA

  

ACACGAAA(-)

6.6

4.5

0.1081

57/55/867

 

CGCGAAAA

CACGAAAA

  

CACGAAAA(+)

7.1

5.5

0.1053

32/57/867

 

CACGAAAA

ACACGAAA

 

CGCGAAA [60]

CGCGAAA(*)

14.9

10.6

0.132

3/2/199

   
  

ACGCGAAA(*)

15.2

10.3

0.1733

1/15/867

   
  

CGCGAAAA(+)

17.7

9.4

0.1352

4/34/867

   

Fkh1, Fkh2

GTAAACA [25]

GTAAACA(+)

8.2

7.4

0.084

8/10/199

GTAAACA

GTAAACAA

GTAAACAA

  

GGTAAACA(+)

7.2

4.6

0.1578

48/21/867

 

ATAAACAA

AATAAACA

 

GTAAACAA [60]

GTAAACAA(*)

9

6.6

0.098

11/66/867

 

AATAAACA

 
 

ATAAACAA [60]

ATAAACAA(*)

8.8

5.9

0.0657

23/142/867

   

MCM1

TTTCCTAA [25]

TTTCCTAA(+)

5.5

5.2

0.0435

35/307/867

N/A

N/A

N/A

Ste12

TGAAACA [61]

TTGAAACA(*)

4.3

4.2

0.0647

66/145/867

N/A

N/A

N/A

  

TGAAACAA(*)

5

4.8

0.0631

46/149/867

   

Met4, Met28

TCACGTG [62]

TCACGTG(-)

5

1.7

0.0845

129/9/199

N/A

N/A

N/A

Cbf1

 

GTCACGTG(-)

5

0.9

0.2205

661/3/867

   
  1. The first two columns list the known TFs and the known binding motifs. The next five columns report the results from WordSpy, followed by the last three columns for the results from MobyDick, RSA tools, and Weeder. The motifs discovered by WordSpy are marked with (+) if on the up strand, (-) if on the down strand or (*) if on both strands. Rank is based on Z g -score and G-score, where the first number is the ranking on Z g -score and the second is on G-score and the third is the total number of discovered motifs of the same length.
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Genome Biology

ISSN: 1474-760X

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