GNNenrich: a novel method for pathway enrichment analysis based on graph neural network.

ABSTRACT:

Motivation

Graph neural network (GNN) models have emerged in many fields and notably for biological networks constituted by genes or proteins and their interactions. The majority of enrichment study methods apply over-representation analysis and gene/protein set scores according to the existing overlap between pathways. Such methods neglect knowledges coming from the interactions between the gene/protein sets. Here, we introduce a novel GNN-based enrichment analysis method called GNNenrich. GNNenrich, through multiple levels of embedding that integrate protein sequence properties and interactions network, establishes functional relationship to support biological interpretation.

Results

GNNenrich have been tested and compared to over-representation analysis technique (g:Profi

SUBMITTER: Mziou-Sallami M 

PROVIDER: S-EPMC12448840 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature