ArticleGenome biology2022
Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
33 citing papers in PubMed.
- Scalable joint non-negative matrix factorization for paired single cell gene expression and chromatin accessibility data.NAR genomics and bioinformatics · 2026Article
- Inference of spatial chromatin accessibility via integration of spatial transcriptomics and single-cell multi-omics data.Nature communications · 2026Article
- Predicting enhancer-gene links from single-cell multi-omics data by integrating prior Hi-C information.Nucleic acids research · 2026Article
- Benchmarking component choices for unpaired single cell RNA and epigenomic integration.Genome biology · 2026Article
- CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Advances in scCUT&Tag and computational analysis for single-cell gene regulatory element mapping.Briefings in bioinformatics · 2026Review
- Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN.Genome research · 2026Article
- Article
- Techniques to detect physical interactions between genomic regions.Epigenomics · 2025Review
- Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data.Nature biotechnology · 2025Article
- High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration.Genome research · 2025Article
- Integration of single cell multiomics data by deep transfer hypergraph neural network.Briefings in functional genomics · 2025Article
- Single-cell omics: experimental workflow, data analyses and applications.Science China. Life sciences · 2025Review
- Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation.bioRxiv : the preprint server for biology · 2024Article
- Single cell variant to enhancer to gene map for coronary artery disease.medRxiv : the preprint server for health sciences · 2024Article
- GEEES: inferring cell-specific gene-enhancer interactions from multi-modal single-cell data.Bioinformatics (Oxford, England) · 2024Article
- Gene regulatory networks in disease and ageing.Nature reviews. Nephrology · 2024Review
- Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data.Briefings in bioinformatics · 2024Article
- A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data.Briefings in bioinformatics · 2024Review
- Liam tackles complex multimodal single-cell data integration challenges.Nucleic acids research · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory potential, for single cell multiome data. This concept is further used for the construction of subpopulation-specific cis-regulatory networks. The capability of inferring useful regulatory network is demonstrated by the two-fold increment on network inference accuracy compared to the Pearson correlation-based method and the 27-fold enrichment of GWAS variants for inflammatory bowel disease in the cis-regulatory elements. The R package scREG provides comprehensive functions for single cell multiome data analysis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.