Benchmarking EGF signaling pathway inference using phosphoproteomics and kinase-substrate interactions.

ABSTRACT: Signaling pathways are useful models for interpreting molecular data, but their coverage has long been constrained by classic biochemistry methods. The growing corpus of kinase-substrate interactions, coupled to phosphoproteomics improvements, pave the way to revisit classic signaling pathways. In this study, we explore context-specific signaling pathway inference from phosphoproteomics and kinase-substrate networks. Focusing on epidermal growth factor (EGF), we conduct a meta-analysis and generate three datasets representing the most comprehensive characterization of the EGF response to date. We infer kinase-kinase pathways and compare them to different ground truth sets. Literature-curated networks consistently yield the highest recovery of ground-truth interactions, with modest gains fr

SUBMITTER: Garrido-Rodriguez M 

PROVIDER: S-EPMC12949236 | biostudies-literature | 2026 Feb

REPOSITORIES: biostudies-literature