ArticleNucleic acids research2025
scProAtlas: an atlas of multiplexed single-cell spatial proteomics imaging in human tissues.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Neutrophils in cancer.Nature reviews. Cancer · 2026Review
- Spatium: A Protein Language Foundation Model for Spatial Proteomics.bioRxiv : the preprint server for biology · 2026Article
- A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation.Nature communications · 2026Article
- Spotlight on challenges and novel methods in highly multiplexed tissue imaging-based spatial proteomics.Journal of translational medicine · 2026Review
- Decoding the breast cancer microenvironment by spatial multi-omics: from architecture to clinical translation.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Review
- The PVAT-MAMs Axis in Atherosclerosis: A Hypothesis-Driven Cross-Scale Conceptual Framework.International journal of molecular sciences · 2026Review
- The good, the bad, and the ugly: opportunities, challenges, and pitfalls in spatial proteomics modeling.Briefings in bioinformatics · 2026Review
- Spatial omics for profiling the dynamic tumor microenvironment.Clinical & translational immunology · 2026Review
- Resolving tissue and cellular functions of parasitic nematodes.Trends in parasitology · 2025Review
- Omics-based Approach Towards Macrophages: New Perspectives of Biology and Function in the Normal and Diseased Heart.International journal of biological sciences · 2025Review
- Inflammatory Cell Interactions in the Rotator Cuff Microenvironment: Insights From Single-Cell Sequencing.International journal of genomics · 2025Review
- Single-cell genomics and spatial transcriptomics in islet transplantation for diabetes treatment: advancing towards personalized therapies.Frontiers in immunology · 2025Review
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Spatial proteomics can visualize and quantify protein expression profiles within tissues at single-cell resolution. Although spatial proteomics can only detect a limited number of proteins compared to spatial transcriptomics, it provides comprehensive spatial information with single-cell resolution. By studying the spatial distribution of cells, we can clearly obtain the spatial context within tissues at multiple scales. Spatial context includes the spatial composition of cell types, the distribution of functional structures, and the spatial communication between functional regions, all of which are crucial for the patterns of cellular distribution. Here, we constructed a comprehensive spatial proteomics functional annotation knowledgebase, scProAtlas (https://relab.xidian.edu.cn/scProAtlas/#/), which is designed to help users comprehensively understand the spatial context within different tissue types at single-cell resolution and across multiple scales. scProAtlas contains multiple modules, including neighborhood analysis, proximity analysis and neighborhood network, to comprehensively construct spatial cell maps of tissues and multi-modal integration, spatial gene identification, cell-cell interaction and spatial pathway analysis to display spatial variable genes. scProAtlas includes data from eight spatial protein imaging techniques across 15 tissues and provides detailed functional annotation information for 17 468 394 cells from 945 region of interests. The aim of scProAtlas is to offer a new insight into the spatial structure of various tissues and provides detailed spatial functional annotation.
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Registered trials
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