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Table 2 Summary of results comparing c-REDUCE and f-REDUCE oligo predictions for ChIP-chip yeast data (part 2).

From: c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression

TF

Motif

Condition

c-REDUCE

f-REDUCE

PUT3

CGGN(11)CCG

YPD

 

1: GVVCG 35.2

    

2: CVCVG 15.1

  

H2O2Lo

  
  

SM

  

RGT1

CGGANNA/TNNTCCG

YPD

 

2: CCHCV 10.8

  

GAL

  

RIM101

TCGGAAG/CTTCCGA

YPD

  
  

H2O2Lo

  
  

H2O2Hi

  

RLM1

CTAWWWWTAG/

YPD

1: TATTT 11.8

1: DTTWA 24.4

 

CTAWWWWTAG

 

2: AARAW 7.5

2: AAVHTA 10.9

   

3: RAWTT 5.7

 
   

5: TTTYY 4.0

 
  

BUT14

  

ROX1

YSYATTGTT/AACAATRSR

YPD

  
  

H2O2Lo

  
  

H2O2Hi

  

RPH1

CCCCTTAAGG/

YPD

  
 

CCTTAAGGGG

H2O2Lo

  
  

H2O2Hi

1: CCCCT 16.1

 
   

3: AAGGGG 3.8

 
  

SM

  

RTG3

GGTCAC/GTGACC

YPD

  
  

H2O2LO

  
  

H2O2HI

  
  

RAPA

4: RTGAC 2.6

 
  

SM

  

SKO1

ACGTCA/TGACGT

YPD

2: ACGTCAT 5.1

1: VCGBC 19.0

    

4: ATGACGT 3.1

SMP1

ACTACTAWWWWTAG/

YPD

3: TTAATAG 6.3

2: TTTHA 9.4

 

CTAWWWWTAGTAGT

   

STP1

RCGGCNNNRCGGC/

YPD

  
 

GCCGYNNNNGCCGY

SM

2: CGGCAY 3.0

 
   

4: TMAGR 2.7

 
   

5: RCGGY 2.2

 

SWI5

KGCTGR/YCAGCM

YPD

3: TGGCTGG 2.5

2: CBDGC 4.7

    

3: GKSTG 1.4

UGA3

CCGNNNNCGG

YPD

  
  

RAPA

  
  

SM

  

XBP1

CTTCGAG/CTCGAAG

YPD

  
  

H2O2Lo

1: TCGAG 27.9

 
   

5: TCGAR 7.3

 

YAP3

TTACTAA/TTAGTAA

YPD

  
  

H2O2Hi

  

YAP5

TTACTAA/TTAGTAA

YPD

  
  

H2O2Hi

  

YAP6

TTACTAA/TTAGTAA

YPD

  
  

H2O2Lo

  
  

H2O2Hi

  

YHP1

TAATTG/CAATTA

YPD

  

YOX1

YAATA/TATTR

YPD

  
  1. See Table 1 for details.