Table 2 Performance of Stubb, D2Z-set, and CSam on 33 data sets in our benchmark
From: Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
|  |  |  |  | Stubb§ | D2Z-set§ | CSam§ | |||
|---|---|---|---|---|---|---|---|---|---|
Data set | Sequence number* | Length†| Maximum sensitivity‡ | P-value | Sensitivity | P-value | Sensitivity | P-value | Sensitivity |
MAPPING3.ADULT | 34 | 254,800 | 0.71 | 0.01 | 0.20 | 0.72 | 0.07 | 0.15 | 0.13 |
mapping1.adult mesoderm | 5 | 28,085 | 0.76 | 0.51 | 0.05 | 0.11 | 0.22 | 0.51 | 0.05 |
mapping1.amnioserosa | 7 | 49,635 | 0.84 | 0.25 | 0.15 | 0.34 | 0.12 | 0.09 | 0.23 |
MAPPING1.BLASTODERM | 77 | 698,840 | 0.77 | 0.00 | 0.36 | 0.10 | 0.13 | 0.00 | 0.26 |
MAPPING1.CARDIAC MESODERM | 8 | 42,979 | 0.76 | 0.08 | 0.22 | 0.03 | 0.28 | 0.12 | 0.19 |
MAPPING1.CNS | 34 | 352,108 | 0.80 | 0.48 | 0.10 | 0.01 | 0.20 | 0.02 | 0.18 |
mapping1.dorsal ectoderm | 8 | 67,490 | 0.77 | 0.08 | 0.22 | 0.88 | 0.00 | 0.08 | 0.22 |
MAPPING1.ECTODERM | 37 | 311,000 | 0.72 | 0.01 | 0.20 | 0.00 | 0.20 | 0.00 | 0.21 |
MAPPING2.ECTODERM | 51 | 416,473 | 0.74 | 0.01 | 0.18 | 0.05 | 0.15 | 0.00 | 0.23 |
MAPPING1.ENDODERM | 16 | 92,723 | 0.82 | 0.01 | 0.24 | 0.31 | 0.12 | 0.01 | 0.26 |
MAPPING1.EYE | 6 | 49,494 | 0.70 | 1.00 | 0.00 | 0.48 | 0.08 | 0.02 | 0.32 |
mapping2.eye | 18 | 156,531 | 0.69 | 0.19 | 0.14 | 0.68 | 0.07 | 0.88 | 0.04 |
mapping1.fat body | 5 | 22,831 | 0.93 | 0.14 | 0.20 | 1.00 | 0.00 | 0.45 | 0.09 |
MAPPING1.FEMALE GONAD | 10 | 44,269 | 0.62 | 0.03 | 0.24 | 0.97 | 0.00 | 0.86 | 0.02 |
mapping1.glia | 7 | 63,008 | 0.82 | 0.49 | 0.09 | 0.16 | 0.19 | 0.21 | 0.17 |
MAPPING1.IMAGINAL DISC | 47 | 441,597 | 0.77 | 0.55 | 0.09 | 0.00 | 0.20 | 0.24 | 0.12 |
mapping2.imaginal disc | 12 | 149,915 | 0.80 | 0.57 | 0.08 | 0.12 | 0.18 | 0.33 | 0.12 |
MAPPING3.LARVA | 69 | 616,635 | 0.76 | 0.05 | 0.14 | 0.02 | 0.15 | 0.00 | 0.18 |
mapping1.male gonad | 8 | 69,044 | 0.85 | 0.22 | 0.15 | 0.46 | 0.10 | 0.15 | 0.18 |
mapping1.malpighian tubules | 4 | 31,338 | 0.81 | 0.10 | 0.25 | 1.00 | 0.00 | 0.30 | 0.16 |
MAPPING1.MESECTODERM | 5 | 45,712 | 0.83 | 0.18 | 0.20 | 0.43 | 0.10 | 0.00 | 0.46 |
MAPPING1.MESODERM | 16 | 87,140 | 0.72 | 0.02 | 0.21 | 0.09 | 0.17 | 0.22 | 0.13 |
MAPPING2.MESODERM | 45 | 233,441 | 0.75 | 0.00 | 0.22 | 0.00 | 0.20 | 0.02 | 0.16 |
MAPPING1.NEUROECTODERM | 7 | 40,315 | 0.80 | 0.01 | 0.34 | 1.00 | 0.00 | 0.00 | 0.51 |
MAPPING2.NEURONAL | 54 | 534,081 | 0.78 | 0.24 | 0.12 | 0.00 | 0.19 | 0.00 | 0.26 |
MAPPING1.PNS | 24 | 234,532 | 0.78 | 0.03 | 0.19 | 0.07 | 0.17 | 0.01 | 0.21 |
mapping2.reproductive system | 21 | 154,400 | 0.69 | 0.16 | 0.14 | 0.34 | 0.10 | 0.24 | 0.12 |
mapping1.salivary gland | 6 | 47,232 | 0.74 | 0.55 | 0.06 | 1.00 | 0.00 | 0.36 | 0.11 |
MAPPING1.SOMATIC MUSCLE | 12 | 86,317 | 0.79 | 0.29 | 0.12 | 0.05 | 0.21 | 0.01 | 0.28 |
mapping1.tracheal system | 9 | 111,351 | 0.85 | 0.55 | 0.08 | 0.21 | 0.16 | 0.18 | 0.17 |
MAPPING1.VENTRAL ECTODERM | 12 | 84,154 | 0.77 | 0.00 | 0.38 | 0.32 | 0.12 | 0.01 | 0.27 |
MAPPING1.VISCERAL MESODERM | 12 | 54,278 | 0.77 | 0.46 | 0.10 | 0.32 | 0.12 | 0.01 | 0.28 |
MAPPING2.WING | 33 | 340,094 | 0.78 | 0.14 | 0.13 | 0.00 | 0.23 | 0.00 | 0.22 |