Table 1 |
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|
Over-represented motifs from ChIP data |
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| ChIP TF |
Phase |
Over-represented motifs (exponential part of p-value without multiplicity correction) |
Known motif |
Known TF |
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|
|
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| FKH1 |
All |
GTAAACA (-23) |
GTAAACAA (-23) |
AATAAACA (-10) |
TAAACAAA |
Fkh1 [15] |
||
| FKH2 |
SG2 |
TAAACAA (-11) |
GTAAACAAA |
Fkh1, Fkh2 [20,21] |
||||
| FKH2 |
G2M |
GTAAACA (-14) |
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| FKH2 |
All |
GTAAACA (-25) |
GTAAACAA (-22) |
AAATAAACA (-12) |
ATAAACAA (-09) |
CGCGTC (-09) |
||
| NDD1 |
G2M |
GTAAACA (-09) |
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| NDD1 |
All |
GTAAACA (-09) |
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| 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)* |
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| 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] |
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|
|
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|
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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|
Kato et al. Genome Biology 2004 5:R56 doi:10.1186/gb-2004-5-8-r56 |
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