Table 1 SignalingProfiler 2.0 parameters

Regulons’ sources

Regulons’ databases for Transcription Factors Enrichment Analysis (TFEA) or Kinase Substrates Enrichment Analysis (KSEA) (Supplementary Fig. 1)

Hypergeometric test*

Boolean, using hypergeometric test on VIPER output to weight the inferred activity according to the number of significantly modulated analytes in the regulon

VIPER correction with proteomics*

Boolean, adjust VIPER output based on proteomics fold-change of analytes. If VIPER returns non-significant modulation but the same modulation is significant in proteomics, include the analyte in VIPER result

Normalize phosphoproteomics*

Boolean, correct phosphoproteomics using proteomics data, reducing the importance of phosphosites equally modulated in both datasets

Phosphosites regulating activity

Boolean, in PhosphoScore computation use regulatory phosphosites that affect only protein activity or both activity and abundance (Supplementary Fig. 1)

Kinome Atlas integration*

Boolean, indicating if PKN contains kinase-substrate relations from the

Ser/Thr Kinome Atlas²⁸ (Supplementary Fig. 3)

Include only direct iteractions

Boolean, keeping only direct interactions in the PKN (Supplementary Fig. 3)

Preprocess PKN*

Boolean, excluding interactions between proteins not quantified in experimental data

Naïve network types*

Distinguished by layer numbers (one, two, three, Supplementary Fig. 3)

Shortest path maximum length*

Maximum distance between two set of molecules forming a layer in the naive network (Supplementary Fig. 3)

Include interactions between shortest paths (connect_all)*

Boolean, incorporate interactions among proteins identified along distinct shortest paths

CARNIVAL types*

CARNIVAL algorithms types (inverse, vanilla one-shot, vanilla two-shots, vanilla three-shots) (Supplementary Fig. 3)

ProxPath preprocessing*

Boolean, exclude paths between model proteins and phenotypes that contain undetected proteins in experimental data

Protein-phenotype path length*

Path length between model proteins and phenotypes

Z-score statistic*

Statistics (mean or median) utilized for randomization in ProxPath (refer to²⁵)

Remove cascades*

Boolean, consider only model proteins independently regulating the phenotype

Weight protein contribution*

Boolean, weight protein activity contribution to phenotype based on the number of regulatory paths

Use CARNIVAL activity*

Boolean, consider only experimentally inferred proteins (derived in Step1) or all network proteins (with CARNIVAL activity) in phenotypic activity computation