Nested co-expression network analysis identifies compact gene clusters in a black box.
Where this comes from
- Record sourced from PubMed, PMID 41934621.
- Also identified by DOI 10.1093/bioinformatics/btag167 and PMC identifier 13163169.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Digital analysis of biological systems requires methods capable of identifying both broad and nested gene modules reflecting complex biological processes. Existing transcriptomic methods often miss compact gene sets corresponding to subprocesses in specialized cell types, limiting insights into functional heterogeneity. We present Nested-WGCNA, a two-stage unsupervised network analysis algorithm designed to identify coarse-grained and fine-grained gene modules. Applied to bulk RNA-Seq data, Nested-WGCNA reveals stable modules reproducible across datasets. When validated against scRNA-Seq data, these modules correspond to both major and minor immune cell subtypes. Application to immunotherapy response datasets uncovers predictive and prognostic biomarkers, highlighting its utility in treatment stratification and biomarker discovery. The NestedWGCNA source code and analysis pipeline are available on GitHub (https://github.com/ilyada/NestedWGCNA) and archived on Zenodo (https://doi.org/10.5281/zenodo.18959244).
Medical subject headings
- Gene Regulatory Networks
- Gene Expression Profiling
- Computational Biology
- Multigene Family