ArticleiScience2021
How many markers are needed to robustly determine a cell's type?
Article in iScience, 2021. 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 30 papers, 2 of them syntheses that pooled it.
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
30 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Meta-analysis of single-cell RNA sequencing co-expression in human neural organoids reveals their high variability in recapitulating primary tissue.PLoS biology · 2024Pooled it
- Learning single-cell chromatin accessibility profiles using meta-analytic marker genes.Briefings in bioinformatics · 2023Pooled it
- The misplaced mouse Pax6 interneuron subclass: A cross-species transcriptomic reassignment.iScience · 2026Article
- Long-term effects of adolescent risperidone treatment on the mouse cortex.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2026Article
- A consensus atlas of human brain development defines cell type-specific maturation trajectories across the lifespan.bioRxiv : the preprint server for biology · 2026Article
- Conserved and specialized features of thalamocortical wiring revealed by single-cell projection mapping in mouse and marmoset.bioRxiv : the preprint server for biology · 2026Article
- Cluster replicability in single-cell and single-nucleus atlases of the mouse brain.Nature communications · 2026Article
- A Mouthful of Genomic Data: Single-Cell Insights into Salivary Gland Biology and Disease.Biology · 2026Review
- Identity crisis: exploring the boundaries of cell type identification in the age of single-cell transcriptomics.Frontiers in cellular neuroscience · 2026Article
- Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data.NPJ precision oncology · 2025Article
- Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas.Nature genetics · 2025Article
- Impact of Cattle Breed in scRNA-Seq Reference on Muscle Fiber Type Deconvolution from Bulk RNA-Seq: A Comparison of Software Tools.Biotech (Basel (Switzerland)) · 2025Article
- Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex.Cell genomics · 2025Article
- scEVE: a single-cell RNA-seq ensemble clustering algorithm capitalizing on the differences of predictions between multiple clustering methods.NAR genomics and bioinformatics · 2025Article
- Genomic and Behavioral Signatures of Selection for Ethanol Preference from the Heterogeneous Stock Collaborative Cross Mice - The Central Nucleus of the Amygdala.Addiction neuroscience · 2025Article
- COME: contrastive mapping learning for spatial reconstruction of single-cell RNA sequencing data.Bioinformatics (Oxford, England) · 2025Article
- Single-nucleus transcriptomics reveals time-dependent and cell-type-specific effects of psilocybin on gene expression.bioRxiv : the preprint server for biology · 2025Article
- Translational Insights From Cell Type Variation Across Amygdala Subnuclei in Rhesus Monkeys and Humans.The American journal of psychiatry · 2024Article
- Lessons about physiological relevance learned from large-scale meta-analysis of co-expression networks in brain organoids.PLoS biology · 2024Article
- CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis.Briefings in bioinformatics · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
Abstract
Our understanding of cell types has advanced considerably with the publication of single-cell atlases. Marker genes play an essential role for experimental validation and computational analyses such as physiological characterization, annotation, and deconvolution. However, a framework for quantifying marker replicability and selecting replicable markers is currently lacking. Here, using high-quality data from the Brain Initiative Cell Census Network (BICCN), we systematically investigate marker replicability for 85 neuronal cell types. We show that, due to dataset-specific noise, we need to combine 5 datasets to obtain robust differentially expressed (DE) genes, particularly for rare populations and lowly expressed genes. We estimate that 10 to 200 meta-analytic markers provide optimal downstream performance and make available replicable marker lists for the 85 BICCN cell types. Replicable marker lists condense interpretable and generalizable information about cell types, opening avenues for downstream applications, including cell type annotation, selection of gene panels, and bulk data deconvolution.
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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.