ArticleCommunications biology2022
Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis.
Article in Communications biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- 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
- Smoothie: efficient inference and integration of spatial co-expression networks from denoised spatial transcriptomics data.Communications biology · 2026Article
- Pitfalls in analysis and interpretation of single-cell RNA-seq data in cancer.Neuro-oncology advances · 2026Review
- Epromoters bind key stress-related transcription factors to regulate clusters of stress response genes.The EMBO journal · 2026Article
- Identification of novel type 1 and type 2 diabetes genes by co-localization of human islet eQTL and GWAS variants with colocRedRibbon.Cell genomics · 2025Article
- Topological and functional characterization of human translation efficiency covariation network.Bioinformatics (Oxford, England) · 2025Article
- Exploring the omnigenic architecture of selected complex traits.American journal of human genetics · 2025Article
- Cell type heterogeneity in gene co-expression networks: implications for toxicological research.Briefings in bioinformatics · 2025Review
- Different nontarget-site mechanisms underlie resistance to dicamba and 2,4-D in an Amaranthus tuberculatus population.Pest management science · 2025Article
- Domain-specific embeddings uncover latent genetics knowledge.bioRxiv : the preprint server for biology · 2025Article
- Mapping the functional network of human cancer through machine learning and pan-cancer proteogenomics.Nature cancer · 2025Article
- Co-regulation and synteny of GFM2 and NSA2 links ribosomal function in mitochondria and the cytosol with chronic kidney disease.Molecular medicine (Cambridge, Mass.) · 2024Review
- Molecular models of bidirectional promoter regulation.Current opinion in structural biology · 2024Review
- A versatile functional interaction between electrically silent KCellular and molecular life sciences : CMLS · 2024Article
- KCNQ1 is an essential mediator of the sex-dependent perception of moderate cold temperatures.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Aberrant gene expression yet undiminished retinal ganglion cell genesis in iPSC-derived models of optic nerve hypoplasia.Ophthalmic genetics · 2024Article
- Sex-biased gene expression at single-cell resolution: cause and consequence of sexual dimorphism.Evolution letters · 2023Article
- Multimodal single cell analysis infers widespread enhancer co-activity in a lymphoblastoid cell line.Communications biology · 2023Article
- Prediction of gene co-expression from chromatin contacts with graph attention network.Bioinformatics (Oxford, England) · 2022Article
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3 authors.
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Abstract
Most human genes are co-expressed with a nearby gene. Previous studies have revealed this local gene co-expression to be widespread across chromosomes and across dozens of tissues. Yet, so far these studies used bulk RNA-seq, averaging gene expression measurements across millions of cells, thus being unclear if this co-expression stems from transcription events in single cells. Here, we leverage single cell datasets in >85 individuals to identify gene co-expression across cells, unbiased by cell-type heterogeneity and benefiting from the co-occurrence of transcription events in single cells. We discover >3800 co-expressed gene pairs in two human cell types, induced pluripotent stem cells (iPSCs) and lymphoblastoid cell lines (LCLs) and (i) compare single cell to bulk RNA-seq in identifying local gene co-expression, (ii) show that many co-expressed genes - but not the majority - are composed of functionally related genes and (iii) using proteomics data, provide evidence that their co-expression is maintained up to the protein level. Finally, using single cell RNA-sequencing (scRNA-seq) and single cell ATAC-sequencing (scATAC-seq) data for the same single cells, we identify gene-enhancer associations and reveal that >95% of co-expressed gene pairs share regulatory elements. These results elucidate the potential reasons for co-expression in single cell gene regulatory networks and warrant a deeper study of shared regulatory elements, in view of explaining disease comorbidity due to affecting several genes. Our in-depth view of local gene co-expression and regulatory element co-activity advances our understanding of the shared regulatory architecture between genes.
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