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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].
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