ArticleBMC bioinformatics2021
GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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39 citing papers in PubMed, 1 synthesis or guideline pooled it, 62 citations in OpenAlex.
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- Multi-omics to study chronic respiratory diseases and viral infections.European respiratory review : an official journal of the European Respiratory Society · 2026Review
- Copula modeling of gene coexpression in single-cell RNA sequencing data.bioRxiv : the preprint server for biology · 2025Article
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- AraceaeDB: a functional genomics database of the Araceae family with a focus on konjac glucomannan biosynthesis inHorticulture research · 2025Article
- DiffCoRank: a comprehensive framework for discovering hub genes and differential gene co-expression in brain implant-associated tissue responses.BMC bioinformatics · 2025Article
- Comprehensive transcriptional analysis of ethylene and softening regulation in plums with distinct climacteric ripening behaviors.BMC plant biology · 2025Article
- TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT) enables automated assessment of global gene regulation linked to disparate expression in user defined genes and gene sets.NAR genomics and bioinformatics · 2025Article
- Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks.BMC bioinformatics · 2025Article
- A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep.Genomics, proteomics & bioinformatics · 2025Article
- Novel effects of reverse transcriptase inhibitor supplementation in skeletal muscle of old mice.Physiological genomics · 2025Article
- Integrated gene co-expression network analysis and experimental validation identified integrin beta 1 as a candidate gene affecting milk production in dairy cattle.Journal of animal science · 2025Article
- Fine construction of gene coexpression network analysis using GTOM and RECODE detected a critical module of neuroblastoma stages 4 and 4S.Hereditas · 2024Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNetwork-based analysis of gene expression through co-expression networks can be used to investigate modular relationships occurring between genes performing different biological functions. An extended description of each of the network modules is therefore a critical step to understand the underlying processes contributing to a disease or a phenotype. Biological integration, topology study and conditions comparison (e.g. wild vs mutant) are the main methods to do so, but to date no tool combines them all into a single pipeline.
resultsHere we present GWENA, a new R package that integrates gene co-expression network construction and whole characterization of the detected modules through gene set enrichment, phenotypic association, hub genes detection, topological metric computation, and differential co-expression. To demonstrate its performance, we applied GWENA on two skeletal muscle datasets from young and old patients of GTEx study. Remarkably, we prioritized a gene whose involvement was unknown in the muscle development and growth. Moreover, new insights on the variations in patterns of co-expression were identified. The known phenomena of connectivity loss associated with aging was found coupled to a global reorganization of the relationships leading to expression of known aging related functions.
conclusionGWENA is an R package available through Bioconductor ( https://bioconductor.org/packages/release/bioc/html/GWENA.html ) that has been developed to perform extended analysis of gene co-expression networks. Thanks to biological and topological information as well as differential co-expression, the package helps to dissect the role of genes relationships in diseases conditions or targeted phenotypes. GWENA goes beyond existing packages that perform co-expression analysis by including new tools to fully characterize modules, such as differential co-expression, additional enrichment databases, and network visualization.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.