Causal Inference and Annotation of Phosphoproteomics Data in Multiomics Cancer Studies.

ABSTRACT: Protein phosphorylation plays a crucial role in regulating diverse biological processes. Perturbations in protein phosphorylation are closely associated with downstream pathway dysfunctions, whereas alterations in protein expression could serve as sensitive indicators of pathological status. However, there are currently few methods that can accurately identify the regulatory links between protein phosphorylation and expression, given issues like reverse causation and confounders. Here, we present Phoslink, a causal inference model to infer causal effects between protein phosphorylation and expression, integrating prior evidence and multiomics data. We demonstrated the feasibility and advantages of our method under various simulation scenarios. Phoslink exhibited more robust estimates and l

SUBMITTER: Dong Q 

PROVIDER: S-EPMC11889353 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature