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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.