ArticleGenome biology2019
Addressing confounding artifacts in reconstruction of gene co-expression networks.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- Exploring the use of machine and deep learning in genome-wide association studies: a comprehensive review.BioData mining · 2026Review
- Alterations of microRNAs across human and mouse limbic brain areas: molecular mechanisms and biological processes involved in major depressive disorder.Neurobiology of stress · 2026Article
- Transcriptional footprints associated with bud fertility in grapevine development (Vitis vinifera L.).Planta · 2026Article
- Molecular mechanisms associated with rootstock-scion interactions in rubber trees.The plant genome · 2026Article
- Article
- m6AConquer: a consistently quantified and orthogonally validated database for the N6-methyladenosine (m6A) epitranscriptome.Nucleic acids research · 2026Article
- Uncovering coordinated pathway interactions through gene co-differential expression in yeast.Nucleic acids research · 2026Article
- A powerful framework for differential co-expression analysis of general risk factors.Bioinformatics (Oxford, England) · 2025Article
- Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells.Nature communications · 2025Article
- SIGEL: a context-aware genomic representation learning framework for spatial genomics analysis.Genome biology · 2025Article
- Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks.Genome research · 2025Article
- Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis.PLoS biology · 2025Article
- CorrAdjust unveils biologically relevant transcriptomic correlations by efficiently eliminating hidden confounders.Nucleic acids research · 2025Article
- Gene regulatory network inference from CRISPR perturbations in primary CD4Cell genomics · 2024Article
- Transcriptome data are insufficient to control false discoveries in regulatory network inference.Cell systems · 2024Article
- eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis.Cell genomics · 2024Article
- Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome.Genome biology · 2024Article
- SGCP: a spectral self-learning method for clustering genes in co-expression networks.BMC bioinformatics · 2024Article
- Dopamine signaling enriched striatal gene set predicts striatal dopamine synthesis and physiological activity in vivo.Nature communications · 2024Article
- Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles.Nucleic acids research · 2024Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Gene co-expression networks capture biological relationships between genes and are important tools in predicting gene function and understanding disease mechanisms. We show that technical and biological artifacts in gene expression data confound commonly used network reconstruction algorithms. We demonstrate theoretically, in simulation, and empirically, that principal component correction of gene expression measurements prior to network inference can reduce false discoveries. Using data from the GTEx project in multiple tissues, we show that this approach reduces false discoveries beyond correcting only for known confounders.
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Registered trials
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