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Table 2 Performance of AlignACE, BioProspector, MDscan and MEME on mammalian skeletal muscle CRMs. Results are shown for the five TFs, Mef2, Myf, Sp1, SRF and Tef, with experimentally verified binding sites within these CRMs. A correlation coefficient cutoff of 0.6 was used in the merging of highly similar discovered motifs (see Methods). (A) Results before block filtering. The number in parentheses next to the rank of the motif indicates the number of times the motif was found in five MultiFinder runs on this CRM sequence set, and the corresponding group specificity scores and ranks are for the highest ranking motif, from the five runs, matching the previously described motifs [35] for these TFs. (B) Results following the removal of motifs that failed our block filtering step. The numbers in parentheses next to the column header "Rank" are the range of number of motifs found by that motif finder following motif merging from the five runs. The ranking of the motif based on group specificity and the group specificity score are reported for each motif. In both Tables 2A and 2B, below the results for each of these five TFs, the geometric mean and range of group specificity scores from the five size-matched randomly selected sequence sets (see Methods) are listed for each motif finder for comparison.

From: Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data

(A) Without Block Filtering

 

AlignACE

BioProspector

MDscan

MEME

 

Rank

Group

Rank

Group

Rank

Group

Rank

Group

Mef2

1(4)

2.40 × 10-16

-

-

1(5)

5.00 × 10-8

4(5)

6.90 × 10-12

Myf

3(5)

4.10 × 10-8

-

-

3(5)

5.40 × 10-2

24(5)

1.40 × 10-4

Sp1

4(2)

3.80 × 10-8

1(4)

1.10 × 10-8

2(5)

1.70 × 10-3

6(5)

3.60 × 10-11

SRF

3(4)

4.10 × 10-8

-

-

-

-

29(5)

7.20 × 10-4

Tef

-

-

-

-

-

-

63(5)

2.20 × 10-2

Mean

4.52 × 10-3

2.40 × 10-7

8.59 × 10-5

1.02 × 10-3

Range

6.90 × 10-1

7.20 × 10-8

1.40 × 10-1

2.50 × 10-24

2.80 × 10-1

1.40 × 10-9

3.20 × 10-1

1.00 × 10-29

(B) After Block Filtering

 

AlignACE

BioProspector

MDscan

MEME

 

Rank (26–38)

Group

Rank (1)

Group

Rank (4)

Group

Rank (112)

Group

Mef2

1

2.40 × 10-16

-

-

1

5.00 × 10-8

4

6.90 × 10-12

Myf

3

4.10 × 10-8

-

-

3

5.40 × 10-2

24

1.40 × 10-4

Sp1

4

3.80 × 10-8

1

1.10 × 10-8

2

1.70 × 10-3

6

3.60 × 10-11

SRF

2

4.10 × 10-8

-

-

-

-

29

7.20 × 10-4

Tef

-

-

-

-

-

-

49

2.20 × 10-2

Mean

3.32 × 10-3

6.48 × 10-8

8.59 × 10-5

9.30 × 10-4

Range

6.90 × 10-1

6.50 × 10-7

1.00 × 10-1

2.50 × 10-24

2.80 × 10-1

1.40 × 10-9

3.70 × 10-1

1.00 × 10-29