ArticleMolecular systems biology2023
CellNeighborEX: deciphering neighbor-dependent gene expression from spatial transcriptomics data.
Article in Molecular systems biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 36 citations in OpenAlex.
- Microenvironment-aware transcriptome reconstruction in spatial transcriptomics.Nature communications · 2026Article
- Deciphering microenvironmental heterogeneity by scalable Niche Guided Module Discovery.Communications biology · 2026Article
- Spatial imprints of emergent cardiomyocyte states in the pressure-overloaded heart.bioRxiv : the preprint server for biology · 2026Article
- InSituPREP enables 3D single-cell mapping of interaction-associated gene programs in the breast cancer tumor microenvironment.Nucleic acids research · 2026Article
- Integrating Spatial Proteogenomics in Cancer Research.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Spatial remodeling of the tumor immune microenvironment in hepatocellular carcinoma with cirrhosis driven by Treg-CD8⁺T cell crosstalk via the SPP1-ITGA4 axis.Translational oncology · 2026Article
- A spatially informed matrix normal model for gene co-expression analysis in spatial transcriptomics studies.Nucleic acids research · 2025Article
- Decoding cell fate: integrated experimental and computational analysis at the single-cell level.Bioinformatics (Oxford, England) · 2025Review
- sCCIgen: a high-fidelity spatially resolved transcriptomics data simulator for cell-cell interaction studies.Genome biology · 2025Article
- Progenitor neighborhoods function as transient niches to sustain olfactory neurogenesis.Stem cell reports · 2025Article
- Multi-scale and multi-context interpretable mapping of cell states across heterogeneous spatial samples.Nature communications · 2025Article
- Systematic assessment of microenvironment-dependent transcriptional patterns and intercellular communication.Genome biology · 2025Article
- SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution.BMC bioinformatics · 2025Article
- Advancing muscle aging and sarcopenia research through spatial transcriptomics.Osteoporosis and sarcopenia · 2025Review
- An algorithmic perspective on deciphering cell-cell interactions with spatial omics data.Briefings in bioinformatics · 2025Review
- New Insights and Implications of Cell-Cell Interactions in Developmental Biology.International journal of molecular sciences · 2025Review
- Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case Example.Methods in molecular biology (Clifton, N.J.) · 2025Article
- NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis.Nature communications · 2024Article
- Linking signal input, cell state, and spatial context to inflammatory responses.Current opinion in immunology · 2024Review
- SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis.Bioinformatics (Oxford, England) · 2024Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 4 countries.
Funding
Abstract
Cells have evolved their communication methods to sense their microenvironments and send biological signals. In addition to communication using ligands and receptors, cells use diverse channels including gap junctions to communicate with their immediate neighbors. Current approaches, however, cannot effectively capture the influence of various microenvironments. Here, we propose a novel approach to investigate cell neighbor-dependent gene expression (CellNeighborEX) in spatial transcriptomics (ST) data. To categorize cells based on their microenvironment, CellNeighborEX uses direct cell location or the mixture of transcriptome from multiple cells depending on ST technologies. For each cell type, CellNeighborEX identifies diverse gene sets associated with partnering cell types, providing further insight. We found that cells express different genes depending on their neighboring cell types in various tissues including mouse embryos, brain, and liver cancer. Those genes are associated with critical biological processes such as development or metastases. We further validated that gene expression is induced by neighboring partners via spatial visualization. The neighbor-dependent gene expression suggests new potential genes involved in cell-cell interactions beyond what ligand-receptor co-expression can discover.
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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 Socratic graph.