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Table 1 Over-represented motifs from ChIP data

From: Identifying combinatorial regulation of transcription factors and binding motifs

ChIP TF Phase Over-represented motifs (exponential part of p-value without multiplicity correction) Known motif Known TF
FKH1 All GTAAACA (-23) GTAAACAA (-23) AATAAACA (-10)    TAAACAAA Fkh1 [15]
FKH2 SG2 TAAACAA (-11)      GTAAACAAA Fkh1, Fkh2 [20,21]
FKH2 G2M GTAAACA (-14)       
FKH2 All GTAAACA (-25) GTAAACAA (-22) AAATAAACA (-12) ATAAACAA (-09) CGCGTC (-09)   
NDD1 G2M GTAAACA (-09)       
NDD1 All GTAAACA (-09)       
MCM1 G2M TTCCTAA (-11) TTTCCTA (-11) ATTTCC (-09) ATTTCCT (-09)   TTACCNAATTNGGTAA Mcm1 [23]
MCM1 All ATTTCCT (-14) TTCCTAA (-12) TTTCCTAA (-12) ATTTCCTA (-10) AATTTCCT (-09) TTTCCTAATTAGGAAA Mcm1 [15]
MCM1 MG1 ATAATTA (-10)      YAATTA Yox1, Yhp1 [25]
MBP1 G1 ACGCGT (-104) CGCGTC (-100) AACGCGT (-95) ACGCGTC (-75) AAACGCGT (-52) ACGCGT Mbp1, Swi6 [3]
MBP1 All CGCGTC (-97) ACGCGT (-85) AACGCG (-81) AACGCGT (-75) ACGCGTC (-62) CRCGAAA Swi4, Swi6 [3]
SWI4 G1 CGCGAA (-56) CGCGAAA (-55) CGCGTC (-49) ACGCGA (-44) AACGCG (-43)   
SWI4 All CGCGTC (-46) CGCGAAA (-46) ACGCGA (-40) AACGCG (-34) GACGCGA (-32)   
SWI6 G1 ACGCGT (-75) AACGCGT (-69) CGCGTC (-57) ACGCGTC (-52) AAACGCG (-41)   
SWI6 All ACGCGT (-59) CGCGTC (-59) AACGCGT (-50) ACGCGTC (-45) CGACGCG (-37)   
STB1 G1 CGCGAAAA (-50) ACGCGA (-44) AACGCG (-38) CGCGTC (-34) AACGCGT (-33)   
STB1 All CGCGAAAA (-49) ACGCGA (-41) CGCGTC (-32) AACGCG (-32) ACGCGAA (-30)   
STE12 G1 CGCGTC (-19) CGCGAA (-13) ACGCGA (-12)    ATGAAAC Ste12 [34]
STE12 All TGAAACA (-20) GACGCGA (-17) ATGAAAC (-16) ACGCGAA (-10) TGAAACAA (-10) TGAAACA Ste12 [33]
DIG1 All TGAAACA (-22) ATGAAAC (-14) CGCGTC (-11)     
ACE2 All ACCAGCA (-19)      CCAGCA Swi5 [39]
SWI5 G1 ACCAGC (-11)      ACCAGC Ace2, Swi5 [37,38]
SWI5 MG1 CCAGCA (-10)      RRCCAGCR Ace2, Swi5 [1]
SWI5 All ACCAGC (-13) AACCAGC (-12) CCAGCC (-12) CCAGCA (-10) ACCAGCA (-09)   
MTH1 All CAGCAG (-10)*       
MET4 All CACGTG (-29) TCACGTG (-25) ACTGTGG (-22) GTGGCA (-12)   TCACGTG Cbf1, Met4, Met28 [40]
MET31 All TGTGGC (-14)      AAACTGTGG Met31, Met32 [1]
        AAANTGTGGC Met31, Met32 [2]
  1. Over-represented motifs of 6- to 9-mers were extracted from the intersection between ChIP targets of a TF and genes of a cell-cycle phase. The phases are G1, S, S/G2, G2/M, M/G1 or the union of 'All' the phases according to the classification of Spellman et al. [1]. The p-value indicates the degree of over-representation of a motif (without multiplicity correction). Motifs in the same typeface belong to the same group; * indicates motifs that do not belong to any particular group. R is A or G. This table shows ChIP TFs described in the main text but lists only the five highest-ranking motifs. Full results are listed in Table A at [19].