ArticleNature communications2021
The molecular basis, genetic control and pleiotropic effects of local gene co-expression.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity.Communications biology · 2023Pooled it
- Multiomic analysis identifies glutaminolysis-dependent metabolic enhancement of immune memory utilised for vaccine development.Nature communications · 2026Article
- Integrating genetic data with biological insight: A practical guide to cis-Mendelian randomization.American journal of human genetics · 2026Review
- Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation.PLoS genetics · 2026Article
- Loss of long-range co-expression is a common feature in cancer.NPJ systems biology and applications · 2026Article
- Focus on single-gene effects limits discovery and interpretation of complex-trait-associated variants.American journal of human genetics · 2026Article
- Smoothie: efficient inference and integration of spatial co-expression networks from denoised spatial transcriptomics data.Communications biology · 2026Article
- Distinguishing causal from tagging enhancers using single-cell multiome data.medRxiv : the preprint server for health sciences · 2026Article
- Epromoters bind key stress-related transcription factors to regulate clusters of stress response genes.The EMBO journal · 2026Article
- Noncoding rare variant associations with blood traits in 166,740 UK Biobank genomes.Nature genetics · 2025Article
- Molecular evolution of the transcription factor PRDM genes and expression profiles in response to stimulations and spinal cord injury repair in lamprey (Lethenteron reissneri).Immunogenetics · 2025Article
- Pleiotropic expression quantitative trait loci are enriched in enhancers and transcription factor binding sites and impact more genes.Computational and structural biotechnology journal · 2024Article
- Molecular genetics of Dupuytren's contracture.EFORT open reviews · 2024Review
- Disentangling genetic effects on transcriptional and post-transcriptional gene regulation through integrating exon and intron expression QTLs.Nature communications · 2024Article
- Aberrant gene expression yet undiminished retinal ganglion cell genesis in iPSC-derived models of optic nerve hypoplasia.Ophthalmic genetics · 2024Article
- Article
- Integrative approaches based on genomic techniques in the functional studies on enhancers.Briefings in bioinformatics · 2023Review
- Gene communities in co-expression networks across different tissues.PLoS computational biology · 2023Article
- Learning gene networks under SNP perturbation using SNP and allele-specific expression data.bioRxiv : the preprint server for biology · 2023Article
- Multimodal single cell analysis infers widespread enhancer co-activity in a lymphoblastoid cell line.Communications biology · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nearby genes are often expressed as a group. Yet, the prevalence, molecular mechanisms and genetic control of local gene co-expression are far from being understood. Here, by leveraging gene expression measurements across 49 human tissues and hundreds of individuals, we find that local gene co-expression occurs in 13% to 53% of genes per tissue. By integrating various molecular assays (e.g. ChIP-seq and Hi-C), we estimate the ability of several mechanisms, such as enhancer-gene interactions, in distinguishing gene pairs that are co-expressed from those that are not. Notably, we identify 32,636 expression quantitative trait loci (eQTLs) which associate with co-expressed gene pairs and often overlap enhancer regions. Due to affecting several genes, these eQTLs are more often associated with multiple human traits than other eQTLs. Our study paves the way to comprehend trait pleiotropy and functional interpretation of QTL and GWAS findings. All local gene co-expression identified here is available through a public database ( https://glcoex.unil.ch/ ).
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