ArticleBioinformatics (Oxford, England)2024
A Spatial Omnibus Test (SPOT) for Spatial Proteomic Data.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Cellular Neighborhoods Govern Antitumor T-cell Infiltration Following Anti-CTLA-4 in Melanoma with Primary Resistance to Anti-PD-1.Cancer discovery · 2026Trial
- Topological Data Analysis of Spatial Protein Expression in Multiplexed Spatial Proteomics Studies.bioRxiv : the preprint server for biology · 2026Article
- SHADE: A multilevel Bayesian framework for modeling directional spatial interactions in tissue microenvironments.PLoS computational biology · 2026Article
- Detecting clinically relevant topological structures in multiplexed spatial proteomics using TopKAT.Patterns (New York, N.Y.) · 2026Article
- TGF-β-driven T-cell exclusion in ovarian cancer: single-cell and spatial transcriptomic views of immune low-response states.Frontiers in immunology · 2025Review
- Benchmarking Spatial Co-Localization Methods for Single-Cell Multiplex Imaging Data with Applications to High-Grade Serous Ovarian and Triple Negative Breast Cancer.Statistics and data science in imaging · 2025Article
- Statistical analysis of multiple regions-of-interest in multiplexed spatial proteomics data.Briefings in bioinformatics · 2024Article
- Spatial proteomics: unveiling the multidimensional landscape of protein localization in human diseases.Proteome science · 2024Review
- mxfda: a comprehensive toolkit for functional data analysis of single-cell spatial data.Bioinformatics advances · 2024Article
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4 authors.
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Abstract
motivationSpatial proteomics can reveal the spatial organization of immune cells in the tumor immune microenvironment. Relating measures of spatial clustering, such as Ripley's K or Besag's L, to patient outcomes may offer important clinical insights. However, these measures require pre-specifying a radius in which to quantify clustering, yet no consensus exists on the optimal radius which may be context-specific.
resultsWe propose a SPatial Omnibus Test (SPOT) which conducts this analysis across a range of candidate radii. At each radius, SPOT evaluates the association between the spatial summary and outcome, adjusting for confounders. SPOT then aggregates results across radii using the Cauchy combination test, yielding an omnibus P-value characterizing the overall degree of association. Using simulations, we verify that the type I error rate is controlled and show SPOT can be more powerful than alternatives. We also apply SPOT to ovarian and lung cancer studies. AVAILABILITY AND IMPLEMENTATION: An R package and tutorial are provided at https://github.com/sarahsamorodnitsky/SPOT.
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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.