PhuEGO: A Network-Based Method to Reconstruct Active Signaling Pathways From Phosphoproteomics Datasets.

ABSTRACT: Signaling networks are critical for virtually all cell functions. Our current knowledge of cell signaling has been summarized in signaling pathway databases, which, while useful, are highly biased toward well-studied processes, and do not capture context specific network wiring or pathway cross-talk. Mass spectrometry-based phosphoproteomics data can provide a more unbiased view of active cell signaling processes in a given context, however, it suffers from low signal-to-noise ratio and poor reproducibility across experiments. While progress in methods to extract active signaling signatures from such data has been made, there are still limitations with respect to balancing bias and interpretability. Here we present phuEGO, which combines up-to-three-layer network propagation with ego netwo

SUBMITTER: Giudice G 

PROVIDER: S-EPMC11134849 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature