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Table 1 Summary of the transcription factor binding motifs discovered by DEME and MEME

From: Discriminative motif discovery in DNA and protein sequences using the DEME algorithm

Transcription Factor

DEME

MEME

 

(R)

(NBP)

(0-order)

(5th-order)

ABF1

 

x

x

x

GAL4

 

x

  

GCN4

 

x

x

x

GCR1

  

x

x

HAP4

  

x

x

HSF1

 

x

 

x

MBP1

x

x

x

x

MCM1

x

x

x

x

MSN2

 

x

 

x

PHO4

 

x

 

x

RAP1

 

x

x

x

REB1

x

x

x

x

SIP4

 

x

  

STE12

 

x

 

x

SWI4

 

x

 

x

Total

3

13

8

13

  1. The first column is the transcription factor name followed by the results for DEME and MEME. DEME is run using randomly shuffled positive sequences (R) or non-binding probes (NBP) as negative sequences. MEME is run using a 0-order or a 5th-order background model. An 'x' indicates a match between the discovered motif and the reference motif. Results are shown for transcription factors where the reference motif was discovered in at least one DEME or MEME experiment. The last row shows the total number of motifs discovered by each algorithm (out of 25 transcription factors).
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BMC Bioinformatics

ISSN: 1471-2105

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