Table 2 Qualitative comparison of SignalingProfiler 2.0 and existing methods

Omics layers

Transcriptomics

X

X

X

X

X

X

X

X

Proteomics

X

X

Phosphoproteomics

X

X

X

X

Metabolomics

X

Biological resolution

Bulk/Pseudo-bulk

X

X

X

X

X

X

X

X

Single-cell

X

X

X

Omics data used as

Measurements (observations)

X

X

X

Statistical scores (contrast/correlation)

X

X

X

X

X

X

X

Additional input

Does not use additional inputs

X

X

X

X

Accepts additional inputs

X

X

X

X

Requires additional inputs

X

Sign

Directed

X

X

X

Activations/Inhibitions

X

X

X

X

X

X

X

Size

Pathways

X

Large networks

X

X

X

X

X

X

X

X

Biological content

Protein signaling interactions

X

X

X

X

X

X

X

Gene regulatory interactions

X

X

X

X

X

X

Omics to PKN

Direct mapping to nodes

X

X

X

X

X

X

Indirect mapping to nodes

X

X

X

Not‐measured nodes

Estimates unmeasured nodes state

X

X

X

X

X

X

X

Includes unmeasured nodes in output

X

X

X

X

X

X

X

X

Algorithm type

Edge filtering and shortest path

X

X

X

X

Recursive signal propagation and heat diffusion

X

Integer linear programming

X

X

X

X

Neural networks

X

Includes user-defined perturbed nodes

X

X

X

Includes phenotypes

X

X

Includes meta-information on nodes

X

X

X

X

Includes meta-information on edges regarding phosphorylation events

X

X

X