Table 1 Reviews of GRN reconstruction methods and their characteristics
Review | [2] | [4] | [5] | This study |
|---|---|---|---|---|
Number of variables | 100 | ∈ [1643,5950] | ∈ [10,100] | ∈ [300,2000] |
Topologies | Yeast | E. coli & S. cerevisiae & S. aureus | Yeast & E. coli | Synthetic & Yeast & E. coli |
Number of methods compared | 4 | 37 | 29 | 10 |
Simulators | SynTReN | GNW | GNW | Rogers & GNW & SynTReN |
Number of experiments | ∈ [20,200] | ∈ [160,805] | ∈ [10,100] | ∼150 |
Impact of number of experiments | – | – | \(\checkmark \) | \(\checkmark \) |
Impact of noise | – | – | – | \(\checkmark \) |
Dataset availability | – | \(\checkmark \) | – | \(\checkmark \) |
Benchmark extension | – | \(\checkmark \) | – | \(\checkmark \) |
Possibility to change parameters | – | – | – | \(\checkmark \) |