ArticleScientific reports2018
Application of Weighted Gene Co-expression Network Analysis for Data from Paired Design.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers, 3 of them syntheses that pooled it.
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Who cites it
103 citing papers in PubMed, 3 syntheses or guidelines pooled it.
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- Genome-wide transcriptional analysis of rapeseed (Brassica napus L.) responses to heat stress: an integrated RNA-Seq meta-analysis, gene co-expression, and gene regulatory network study.BMC plant biology · 2025Pooled it
- A six‑gene support vector machine classifier contributes to the diagnosis of pediatric septic shock.Molecular medicine reports · 2020Pooled it
- Comparative transcriptome analysis of Qinchuan and Wagyu cattle reveals lnc11599 as a negative regulator of intramuscular fat deposition.BMC genomics · 2026Article
- Bioinformatics and experimental validation of druggable targets in non-alcoholic fatty liver disease.Scientific reports · 2026Article
- Genetic Risk and Resilience for Schizophrenia Stratified by Perinatal Gene Expression Predict Adult Cognitive Performance.bioRxiv : the preprint server for biology · 2026Article
- Identification of shared gene signature between lung cancer and postoperative delirium by transcriptome data analysis.Medicine · 2026Article
- Potential Biological Processes Related to Brain SLC13A5 Across the Lifespan: Weighted Gene Co-Expression Network Analysis from Large Human Transcriptomic Data.Brain sciences · 2026Article
- Temporal network analysis in systems biology: concepts, inference, and validation.Frontiers in bioinformatics · 2026Review
- Mutations of schizophrenia risk gene SETD1A dysregulate synaptic function in human neurons.Molecular psychiatry · 2025Article
- A Comprehensive Profiling of the RicePlants (Basel, Switzerland) · 2025Article
- Endometrial receptivity profiled through transcriptomic analysis of uterine fluid extracellular vesicles using systems biology and bayesian modeling for pregnancy prediction.Scientific reports · 2025Article
- Conserved Blood Transcriptome Patterns Highlight microRNA and Hub Gene Drivers of Neurodegeneration.Genes · 2025Article
- An Introduction to Network Analysis in Plant Biology.Plant direct · 2025Article
- Mechanistic Insights into a Self-Management Intervention in Young Adults with Irritable Bowel Syndrome: A Pilot Multi-Omics Study.Biomedicines · 2025Article
- Uncovering the Understanding of the Concept of Patient Similarity in Cancer Research and Treatment: Scoping Review.Journal of medical Internet research · 2025Article
- From Data Mining to Discovery: SNHG11 as a Therapeutic Target in Pulmonary Hypertension.American journal of respiratory cell and molecular biology · 2025Article
- Comprehensive Bioinformatics Analysis of Glycosylation-Related Genes and Potential Therapeutic Targets in Colorectal Cancer.International journal of molecular sciences · 2025Article
- Identifying Essential Hub Genes and circRNA-Regulated ceRNA Networks in Hepatocellular Carcinoma.International journal of molecular sciences · 2025Article
- Weighted gene co-expression network analysis reveals the hub genes and molecular mechanism of quiescence.3 Biotech · 2025Article
43 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Investigating how genes jointly affect complex human diseases is important, yet challenging. The network approach (e.g., weighted gene co-expression network analysis (WGCNA)) is a powerful tool. However, genomic data usually contain substantial batch effects, which could mask true genomic signals. Paired design is a powerful tool that can reduce batch effects. However, it is currently unclear how to appropriately apply WGCNA to genomic data from paired design. In this paper, we modified the current WGCNA pipeline to analyse high-throughput genomic data from paired design. We illustrated the modified WGCNA pipeline by analysing the miRNA dataset provided by Shiah et al. (2014), which contains forty oral squamous cell carcinoma (OSCC) specimens and their matched non-tumourous epithelial counterparts. OSCC is the sixth most common cancer worldwide. The modified WGCNA pipeline identified two sets of novel miRNAs associated with OSCC, in addition to the existing miRNAs reported by Shiah et al. (2014). Thus, this work will be of great interest to readers of various scientific disciplines, in particular, genetic and genomic scientists as well as medical scientists working on cancer.
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