ArticleNucleic acids research2026
DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments.
Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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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.
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Who cites it
3 citing papers in PubMed.
- Tumor-derived Parathyroid Hormone-Related Protein Is Associated with Suppression of Cytochrome P450 Expression: Evidence From Multimodal Transcriptomics.ACS pharmacology & translational science · 2026Article
- Artificial Intelligence in genomics: a comprehensive survey of methods, resources, challenges, and prospects.Briefings in bioinformatics · 2026Review
- MatriSpace: Identification and visualization of spatially resolved ECM gene expression patterns in health and disease.bioRxiv : the preprint server for biology · 2026Article
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Authors and funding
7 authors.
Funding
Abstract
Spatial transcriptomics enables detailed mapping of gene expression within tissues, revealing spatial organization of cellular and molecular processes. However, generating such data is costly and technically challenging, and analysis requires advanced bioinformatics skills. Although public datasets are growing, existing databases offer limited tools for interactive exploration and cross-sample comparison. Here, we introduce DeepSpaceDB (www.deepspacedb.com), a next-generation spatial transcriptomics database designed to address these challenges. The current version of DeepSpaceDB focuses on 10X Genomics Visium samples, ensuring higher-quality analyses and enhanced tools. This distinguishes it from databases that prioritize broad platform coverage over functionality. Emphasizing interactivity and advanced analytics, DeepSpaceDB enables flexible exploration of spatial transcriptomics data. Users can interactively compare gene expression across regions within or between tissue slices, such as between hippocampal areas of an Alzheimer's model mouse and a control. The database also offers quality indicators, database-wide trends, and interactive visualizations like zoomable plots and hover-based info. Moreover, these functions are not restricted to samples in our database but can also be applied to samples uploaded by users. Combining advanced tools with interactive features, DeepSpaceDB is a powerful resource for spatial transcriptomics, enabling deeper insights into tissue organization and disease biology.
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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.