ArticleGenome biology2025
InSituCor: exploring spatially correlated genes conditional on the cell type landscape.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Spatial transcriptomics identifies immune-stromal niches associated with cancer in adult dermatomyositis.Nature communications · 2026Article
- Single-cell spatial analysis stratifies lung adenocarcinoma with rare actionable mutations and reveals immune-modulatory cellular crosstalk.Cell reports. Medicine · 2026Article
- Ectopic expression of MUC5B in the respiratory bronchiole initiates endoplasmic reticulum stress in the IPF lung.American journal of respiratory cell and molecular biology · 2026Article
- SpatialQuery: scalable discovery and molecular characterization of multicellular motifs from spatial omics data.bioRxiv : the preprint server for biology · 2026Article
- Single-cell and spatial profiling in cancer biology and clinical oncology.Nature cancer · 2026Review
- Spatial multiomics to inform immunocytokine engineering: knowledge base, gaps, and QC solutions.Frontiers in immunology · 2026Review
- Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development.Nature plants · 2026Article
- Single-cell Spatial Transcriptional Profiling Uncovers Heterogeneous Cellular Responses to Pathogenic Tau in a Mouse Model of Neurodegeneration.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
In spatial transcriptomics data, spatially correlated genes promise to reveal high-interest phenomena like cell-cell interactions and latent variables. But in practice, most spatial correlations arise from the spatial arrangement of cell types, obscuring the more interesting relationships we hope to discover. We introduce InSituCor, a toolkit for discovering modules of spatially correlated genes. InSituCor returns only correlations not explainable by already-known factors like the cell type landscape; this spares precious analyst effort. InSituCor supports both unbiased discovery of whole-dataset correlations and knowledge-driven exploration of genes of interest. As a special case, it evaluates ligand-receptor pairs for spatial co-regulation.
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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.