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Table 1 fREDUCE motif predictions from yeast ChIP-chip

From: fREDUCE: Detection of degenerate regulatory elements using correlation with expression

Factor

Known Site

Condition

Motif

p-value

fREDUCE match?

AlignACE Match?

ABF1

rTCAyt....Acg

YPD

rTGATm

22.4

√

√

ACE2

tGCTGGT

YPD

kGCTGGy

6.2

√

 

AFT2

GGGTGy

H2O2Lo

rGGTGy

91.5

√

√

AZF1

YwTTkcKkTyyckgykky

YPD

mTTTTw

14.8

  

BAS1

TGACTC

YPD

TGACTCCG

37.2

√

√

CAD1

mTTAsTmAkC

YPD

GmTTAsTA

4.2

√

√

CBF1

tCACGTG

YPD

CACGTG

90.7

√

√

CIN5

TTAygTAA

YPD

TTAyrTAA

59.4

√

√

DAL82

GATAAGa

RAPA

GATAAG

9.4

√

 

DIG1

TgAAAca

YPD

TGAAACA

18

√

 

FHL1

rTGTayGGrtg

YPD

GTAyGGrT

141.2

√

√

FKH1

tTgTTTac

YPD

yTGTTkAC

28.8

√

 

FKH2

aaa.GTAAACAa

YPD

GTAAACA

23.7

√

√

GAL4

CGG...........cCg

YPD

TTCGGAGC

4.9

 

√

GAT1

aGATAAG

RAPA

GATAAG

13.3

√

 

GCN4

TGAsTCa

YPD

rTGAsTCA

166.7

√

√

GLN3

GATAAGa.a

RAPA

GATAAG

38.2

√

 

HAP1

GGmraTA.CGs

YPD

kTTATCGG

60.3

√

√

HAP4

g.CcAAtcA

YPD

CCAATsAr

21.7

√

√

HSF1

TTCya.....TTC

H2O2Hi

TTCyrGAA

109.5

√

√

IME1

 

H2O2Hi

    

INO2

CAcaTGc

YPD

kCACATGC

12.8

√

 

INO4

CATGTGaaaa

YPD

CAyrTG

89.2

√

√

LEU3

cCGgtacCGG

YPD

CGGkACCG

10.8

√

√

MBP1

rACGCGt

YPD

ACGCGT

126.9

√

√

MCM1

tttCC.rAt..gg

Alpha

yTTCCTAA

5.7

 

√

MET4

RMmAwsTGKSgyGsc

SM

CrCGyG

14.8

  

MSN2

mAGGGGsgg

H2O2Hi

rGGGGy

20.8

√

 

NDD1

tt.CC.rAw..GG

YPD

CTCGAGGC

12.3

 

√

NRG1

GGaCCCT

YPD

AGGGTCs

11.3

√

√

PDR1

ccGCCgRAwra

YPD

CCrwACAT

11.4

  

PHD1

sc.GC.gg

YPD

mTGCAk

21.1

 

√

PHO2

SGTGCGsygyG

Pi-

    

PHO4

CACGTGs

Pi-

sCACGTGs

14.1

√

 

RAP1

tGyayGGrtg

SM

GyrTGGGT

57.1

√

√

RCS1

ggGTGca.t

H2O2Lo

GGGTGCA

43.6

√

√

RDS1

kCGGCCGa

H2O2Hi

TCCGCGG

35.6

√

 

REB1

CGGGTAA

YPD

CGGGTAAy

136.7

√

√

RFX1

TTgccATggCAAC

YPD

GTCGTCCG

3.2

 

√

RLR1

ATTTTCttCwTt

YPD

    

RPN4

TTTGCCACC

H2O2Lo

TyGCCACC

109.8

√

√

SFP1

ayCcrtACay

SM

yCCrTACA

31.6

√

√

SIG1

ArGmAwCrAmAA

H2O2Hi

    

SIP4

CGG.y.AATGGrr

SM

CTCGGCCC

58.4

  

SKN7

G.C..GsCs

H2O2Lo

GsCyGGCC

37.7

√

 

SNT2

yGGCGCTAyca

YPD

GrTAGCGC

96.1

√

√

SOK2

tGCAg..a

BUT14

GGTrCAGA

5.6

  

SPT2

ymtGTmTytAw

YPD

TkyATA

6.2

  

SPT23

rAAATsaA

YPD

wTkAAA

25.1

  

STB1

rracGCsAaa

YPD

wCGCGT

4

√

 

STB4

TCGg..CGA

YPD

CGGryCGA

7.1

√

√

STB5

CGGwstTAta

YPD

CGGkGwTA

24

√

 

STE12

tgAAACa

YPD

TGAAACA

38.9

√

√

SUM1

gyGwCAswaaw

YPD

GyGTCAs

25.0

√

√

SUT1

gcsGsg..sG

YPD

wCkCCG

49.8

  

SWI4

raCgCsAAA

YPD

CGCsAAAA

12.6

√

√

SWI6

tttcGCGt

YPD

TTTCsk

11.6

√

 

TEC1

rrGAATG

YPD

rrGAATGT

22.4

√

 

THI2

gmAAcy.twAgA

Thi-

GGAAACyS

4.5

√

 

TYE7

tCACGTGAy

YPD

TCACGTGr

70.8

√

√

UME6

taGCCGCCsa

YPD

GCsGCy

154.3

√

√

YAP1

TTaGTmAGc

YPD

mTkACTAA

13.6

√

√

YAP7

mTkAsTmAk

H2O2Hi

mTTAsTAA

121.9

√

√

YDR026c

ttTACCCGGm

YPD

CCGGGTAA

23.2

√

√

ZAP1

ACCCTmAAGGTyrT

YPD

wAyATT

16.5

  
  1. fREDUCE predictions from 65 yeast ChIP-chip experiments of Harbison et. al. Check marks (√) indicate that fREDUCE matched the IUPAC string corresponding to the benchmark logo. The results of a similar analysis with AlignACE is given in the right column.