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Table 1 Reviews of GRN reconstruction methods and their characteristics

From: NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference

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 \(\checkmark \)