Table 2 Summary of commonly used open-source causal reasoning algorithms and whether they were included in this study
Algorithm | Description | Input(s) | Output(s) | Included |
|---|---|---|---|---|
CausalR | Nodes scored by counting the number of concordant/discordant interactions Nodes scores are also assessed for statistical significance, returning a p-value | Gene/Protein Z-scores or fold-changes Any signed and directed network | Ranked table of scored nodes with p-values Sub-network of consensus regulators (ScanR) and their concordant interactions | Yes |
SigNet | Ensemble of scoring methods which takes into account log fold-changes | Gene Z-scores or fold-changes Any signed and directed network | Ranked table of scored nodes | Yes |
CARNIVAL | Integer Linear Programming optimisation of a sub-network capturing signalling changes | Gene/Protein Z-scores or fold-changes Any signed and directed network | Optimised sub-network | Yes |
DeMAND | Scores nodes by computing Kullback–Leibler divergence of interacting genes in the network | Treatment and control—level gene expression data Any signed and directed network | Ranked table of scored nodes | No—Different input data required |
ProTINA | ODE (ordinary differential equation) kinetic approximations of mRNA regulation to estimate ability of each node on the network to modulate gene regulatory activity | Gene Z-scores or fold-changes Cell-specific network | Ranked table of scored nodes | No—Different input network required |