A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model
Table 2
The performances of all methods on the REDfly dataset.
Data Set
#Seq, Length, Max. Sens.
ComSPS
MotEvo
Cluster- Buster
CPModule
Stubb
BayCis
mapping1.adult mesoderm
34/254800/0.71
0.34 (0.14)
0.63 (0.05)
0.32 (0.15)
1.00 (0.00)
0.51 (0.05)
0.63 (0.05)
mapping1.amnioserosa
5/28085/0.76
0.00 (0.43)
0.13 (0.13)
0.31 (0.09)
0.09 (0.16)
0.25 (0.15)
1.00 (0.00)
mapping1.blastoderm
7/49635/0.84
0.02 (0.15)
0.00 (0.32)
0.76 (0.07)
0.02 (0.15)
0.00 (0.36)
0.04 (0.14)
mapping1.cardiac mesoderm
77/698840/0.77
0.00 (0.26)
0.09 (0.15)
0.42 (0.07)
0.65 (0.02)
0.08 (0.22)
0.60 (0.03)
mapping1.cns
8/42979/0.76
0.94 (0.04)
0.51 (0.10)
0.15 (0.14)
0.04 (0.17)
0.48 (0.10)
0.63 (0.08)
mapping1.dorsal ectoderm
34/352108/0.80
0.55 (0.08)
0.17 (0.17)
0.04 (0.24)
0.58 (0.08)
0.08 (0.22)
0.90 (0.00)
mapping1.ectoderm
8/67490/0.77
0.72 (0.07)
0.02 (0.16)
1.00 (0.02)
0.09 (0.13)
0.01 (0.20)
0.01 (0.21)
mapping1.endoderm
37/311000/0.72
0.00 (0.47)
0.09 (0.15)
0.44 (0.08)
0.82 (0.03)
0.01 (0.24)
0.67 (0.05)
mapping1.eye
51/416473/0.74
0.01 (0.31)
0.46 (0.07)
1.00 (0.00)
0.01 (0.28)
1.00 (0.00)
0.38 (0.12)
mapping1.fat body
16/92723/0.82
0.14 (0.21)
1.00 (0.00)
0.57 (0.04)
0.37 (0.12)
0.14 (0.20)
0.37 (0.12)
mapping1.female gonad
6/49494/0.70
0.59 (0.04)
0.00 (0.33)
1.00 (0.00)
0.49 (0.05)
0.03 (0.24)
0.02 (0.26)
mapping1.glia
18/156531/0.69
0.00 (0.56)
0.19 (0.13)
1.00 (0.00)
0.09 (0.18)
0.49 (0.09)
1.00 (0.00)
mapping1.imaginal disc
5/22831/0.93
0.00 (0.19)
0.53 (0.07)
0.45 (0.08)
0.18 (0.10)
0.55 (0.09)
0.00 (0.19)
mapping1.male gonad
10/44269/0.62
0.03 (0.24)
0.12 (0.17)
0.48 (0.07)
1.00 (0.00)
0.22 (0.15)
0.55 (0.05)
mapping1.malpighian tubules
7/63008/0.82
0.24 (0.12)
0.02 (0.28)
1.00 (0.00)
0.40 (0.04)
0.10 (0.25)
1.00 (0.00)
mapping1.mesectoderm
47/441597/0.77
0.58 (0.05)
0.14 (0.21)
0.63 (0.03)
0.05 (0.30)
0.18 (0.20)
0.63 (0.03)
mapping1.mesoderm
12/149915/0.80
0.05 (0.19)
0.00 (0.35)
0.69 (0.06)
0.47 (0.10)
0.02 (0.21)
0.34 (0.12)
mapping1.neuroectoderm
69/616635/0.76
0.02 (0.21)
0.00 (0.36)
0.39 (0.06)
0.01 (0.23)
0.01 (0.34)
0.05 (0.16)
mapping1.pns
8/69044/0.85
0.37 (0.11)
0.01 (0.22)
0.50 (0.09)
0.35 (0.11)
0.03 (0.19)
0.39 (0.10)
mapping1.salivary gland
4/31338/0.81
0.27 (0.08)
0.13 (0.12)
0.60 (0.01)
0.61 (0.01)
0.55 (0.06)
0.21 (0.10)
mapping1.somatic muscle
5/45712/0.83
0.29 (0.14)
0.60 (0.08)
0.41 (0.11)
0.55 (0.09)
0.29 (0.12)
0.13 (0.18)
mapping1.tracheal system
16/87140/0.72
0.71 (0.05)
0.55 (0.08)
0.70 (0.05)
0.74 (0.04)
0.55 (0.08)
1.00 (0.00)
mapping1.ventral ectoderm
45/233441/0.75
0.01 (0.23)
0.00 (0.31)
0.17 (0.13)
0.11 (0.15)
0.00 (0.38)
0.44 (0.08)
mapping1.visceral mesoderm
7/40315/0.80
0.04 (0.19)
0.06 (0.18)
1.00 (0.00)
0.64 (0.05)
0.46 (0.10)
0.64 (0.05)
mapping2.ectoderm
54/534081/0.78
0.02 (0.16)
0.08 (0.14)
0.08 (0.14)
0.02 (0.16)
0.01 (0.18)
0.04 (0.15)
mapping2.eye
24/234532/0.78
0.27 (0.12)
0.07 (0.16)
0.43 (0.09)
0.70 (0.06)
0.19 (0.14)
0.34 (0.12)
mapping2.imaginal disc
21/154400/0.69
0.16 (0.10)
0.20 (0.09)
0.00 (0.29)
0.09 (0.12)
0.57 (0.08)
0.63 (0.03)
mapping2.mesoderm
6/47232/0.74
0.62 (0.08)
0.00 (0.24)
0.26 (0.11)
0.12 (0.13)
0.00 (0.22)
0.00 (0.24)
mapping2.neuronal
12/86317/0.79
0.49 (0.09)
0.16 (0.12)
0.90 (0.05)
0.91 (0.05)
0.24 (0.12)
0.72 (0.07)
mapping2.reproductive system
9/111351/0.85
0.00 (0.30)
0.37 (0.08)
0.59 (0.05)
0.02 (0.15)
0.16 (0.14)
0.00 (0.20)
mapping2.wing
12/84154/0.77
0.02 (0.17)
0.14 (0.12)
0.89 (0.04)
0.28 (0.10)
0.14 (0.13)
0.18 (0.11)
mapping3.adult
12/54278/0.77
0.00 (0.20)
0.03 (0.14)
0.05 (0.13)
0.34 (0.09)
0.01 (0.20)
0.05 (0.13)
mapping3.larva
33/340094/0.78
0.97 (0.03)
0.06 (0.11)
1.00 (0.01)
0.24 (0.09)
0.05 (0.14)
0.97 (0.03)
The number of sequences, total length of sequences, and maximum sensitivity of sequences on a subdataset. The empirical value (and sensitivity) of a method’s predictions. Statistically significant predictions ( value ≤ 0.05) are shown in bold.
