Table 1 Overview of performance of several methods and measures for prediction of motif enrichment on artificial and real datasets
Method or measure | Type | Artificial data | Real data | Reference | ||||
|---|---|---|---|---|---|---|---|---|
Recall | Precision | F-measure | Recall | Precision | F-measure | |||
LocaMo Finder (Gaussian) | local | 0.755 | 0.609 | 0.674 | 0.371 | 0.757 | 0.498 | this study |
LocaMo Finder (uniform) | local | 0.727 | 0.519 | 0.606 | 0.343 | 0.723 | 0.465 | this study |
RSAT (Binomial distribution) ($) | global | 0.714 | 0.285 | 0.408 | 0.429 | 0.440 | 0.434 | RSAT [40] |
ORI (**) | global | 0.677 | 0.386 | 0.492 | 0.343 | 0.563 | 0.426 | this study |
Hypergeometric distribution (*) | global | 0.745 | 0.272 | 0.399 | 0.400 | 0.450 | 0.424 | AlignACE [41] |
Fisher’s exact test (*) | global | 0.747 | 0.276 | 0.403 | 0.400 | 0.443 | 0.420 | oPOSSUM [42] |
ORI (*) | global | 0.768 | 0.258 | 0.387 | 0.429 | 0.407 | 0.417 | this study |
RSAT (Binomial distribution) ($$) | global | 0.591 | 0.498 | 0.541 | 0.271 | 0.607 | 0.375 | RSAT [40] |
Hypergeometric distribution (***) | global | 0.605 | 0.522 | 0.560 | 0.243 | 0.706 | 0.361 | AlignACE [41] |
Fisher’s exact test (***) | global | 0.605 | 0.530 | 0.565 | 0.243 | 0.667 | 0.356 | oPOSSUM [42] |
Casimiro et al. | local | 0.727 | 0.053 | 0.099 | 0.629 | 0.132 | 0.218 | [9] |
Berendzen et al. | local | 0.859 | 0.044 | 0.083 | 0.786 | 0.093 | 0.167 | [1] |
Vardhanabhuti et al. | local | 0.409 | 0.079 | 0.133 | 0.314 | 0.090 | 0.139 | [3] |
FIRE (Information content) | global | 0.586 | 0.342 | 0.432 | 0.100 | 0.200 | 0.133 | FIRE [43] |
TFM-Explorer | local | 0.432 | 0.145 | 0.217 | 0.186 | 0.076 | 0.108 | [6] |
FREE | local | 0.155 | 0.182 | 0.167 | 0.029 | 0.013 | 0.018 | [5] |
A-GLAM | local | 0.032 | 0.259 | 0.057 | 0.000 | 0.000 | NA | |