Graph algorithms for predicting subcellular localization at the pathway level

ABSTRACT: Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context. Biological pathways are graphs that represent a specific biological context and can be inferred from large-scale data. We develop graph algorithms to predict the localization of all interactions in a biological pathway as an edge-labeling task. We compare a variety of models including graph neural networks, probabilistic graphical models, and discriminative classifiers for predicting localization annotations from curated pathway databases. We also perform a case study where we construct biological pathways and predict localizations of human fibroblasts und

SUBMITTER: Magnano CS 

PROVIDER: S-EPMC9817068 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature