Table 1 Parameters considered in this benchmarking study, their specific values under investigation, and the scientific aims of investigating each parameter
Parameter | Aim of investigation |
|---|---|
Algorithm | Determine which algorithms perform better, examine how they handle network bias |
Network | Examine effects of coverage vs. potential noise |
Platform | Comparison between two transcriptomics technologies, evaluation of use of L1000 data with causal reasoning |
Gene Set | Evaluation of the ability of reduced representation of transcriptome to gain MoA insights, comparison between inferred vs. measured genes |
Cell Line | Evaluate effect of biological context on the ability of the algorithms to recover diverse MoAs |