System-level network-based approaches are an emerging field in the biomedical domain since biological networks can be used to analyze complicated biological processes and complex human disorders more efficiently. Network biomarkers are groups of interconnected molecular components causing perturbations in the entire network topology that can be used as indicators of pathogenic biological processes when studying a given disease. Although in the last years computational systems-based approaches have gained ground on the path to discovering new network biomarkers, in complex diseases like Alzheimer's disease (AD), this approach has still much to offer. Especially the adoption of single-cell RNA sequencing (scRNA-seq) has now become the dominant technology for the study of stochastic gene expression. Toward this orientation, we propose an R workflow that extracts disease-perturbed subpathways within a pathway network. We construct a gene-gene interaction network integrated with scRNA-seq expression profiles, and after network processing and pruning, the most active subnetworks are isolated from the entire network topology. The proposed methodology was applied on a real AD-based scRNA-seq data, providing already existing and new potential AD biomarkers in gene network context.
Keywords: Alzheimer’s disease; Network biomarkers; differentially expressed pathways; single-cell RNA sequencing.
© 2023. The Author(s), under exclusive license to Springer Nature Switzerland AG.