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Table 1 Classification of the different methodologies and some of their representatives (see [1], [14] for more exhaustive lists)

From: Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models

Reasoning Category Method Qualitative Quantitative Use topology Interpretability Diagnostic Sigs Threshold-free
  ORA Hypergometric test [15]      
   GSEA [2] ()    
  FCS GSA [52] ()    
   PLAGE [16] ()    
Forward   CORG [33]    
   SPIA [46]      
   NetGen [17]     
  PT NetWalker [18]    
   SVM-based [35]     
  ORA RCR [21]      
   Modified GSA [22]    
Backward FCS MARINa [20]     
   NPA [23]    
  PT TopoNPA
  1. For each represented method, their properties are described. The method described in this study, TopoNPA, is to our knowledge the first backward PT methodology. ORA: Over-Representation Analysis, FCS: Functional Class Scoring, PT: Pathway Topology. (): with small modification.