Table 2 |
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|
Comparison between methods. |
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|
A |
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|
|
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|
Method |
Clover |
ModuleSearcher(A*) |
ModuleDigger |
||||||
|
|
|||||||||
|
Running time |
1.6 min |
0.5 min |
10 s |
||||||
|
|
|||||||||
|
NM |
SRR |
Sn |
NM |
SRR |
Sn |
NM |
SRR |
Sn |
|
|
|
|||||||||
|
OCT4, SOX2, NANOG |
0 |
0 |
0 |
2.4 |
10 |
1.1% |
6 |
10 |
27.6% |
|
|
|||||||||
|
OCT4, SOX2 |
3.9 |
10 |
45.3% |
0 |
0 |
0 |
2 |
10 |
49.1% |
|
|
|||||||||
|
OCT4, NANOG |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
10 |
42.2% |
|
|
|||||||||
|
SOX2, NANOG |
0 |
0 |
0 |
2.4 |
10 |
0.9% |
9 |
10 |
28.4% |
|
|
|||||||||
|
|
|||||||||
|
B |
|||||||||
|
|
|||||||||
|
Method |
Clover |
ModuleSearcher (A*) |
ModuleDigger |
||||||
|
|
|||||||||
|
Running time |
4 min |
0.5 min |
20 s |
||||||
|
|
|||||||||
|
NM |
SRR |
Sn |
NM |
SRR |
Sn |
NM |
SRR |
Sn |
|
|
|
|||||||||
|
OCT4, SOX2, NANOG |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
10 |
28% |
|
|
|||||||||
|
OCT4, SOX2 |
6.8 |
10 |
45.3% |
21 |
5 |
2.8% |
18 |
10 |
49% |
|
|
|||||||||
|
OCT4, NANOG |
0 |
0 |
0 |
0 |
0 |
0 |
23 |
10 |
42% |
|
|
|||||||||
|
SOX2, NANOG |
0 |
0 |
0 |
21 |
4 |
0.5% |
20 |
10 |
9% |
|
|
|||||||||
|
(A) For all algorithms we used as input the benchmark set, the PWMs of OCT4, SOX2, NANOG and one random PWM. NM: number of modules present in the output for those runs where the RR = 1 (average over runs where RR = 1). SRR (summation of recovery rate): number of runs for which the output contained a module corresponding to the valid modules (OCT4, SOX2, NANOG or combinations thereof). Sn: number of genes containing the valid module in the output (average of runs for which RR was 1). (B) Similar to (A) but using OCT4, SOX2, NANOG in combination with 7 randomly selected PWMs. |
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|
Sun et al. BMC Bioinformatics 2009 10(Suppl 1):S30 doi:10.1186/1471-2105-10-S1-S30 |
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