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PLAE Web App Enables Powerful Searching and Multiple Visualizations Across One Million Unified Single-Cell Ocular
Vinay S Swamy1, Zachary A Batz2, David M McGaughey3
1Department of Biomedical Informatics, Columbia University, New York, NY, USA.
Translational Vision Science & Technology
|September 25, 2023
Summary
Researchers can now explore gene expression data for over a million cells using the new PLAE web application. This tool facilitates hypothesis testing across diverse eye and body tissues in multiple species.
Area of Science:
- Genomics
- Bioinformatics
- Ophthalmology
Background:
- Single-cell RNA sequencing provides high-resolution gene expression data.
- Integrating diverse datasets is crucial for comprehensive biological insights.
- Existing resources may lack unified access to cross-species transcriptomic data.
Purpose of the Study:
- To develop a high-performance web application for querying single-cell gene expression data.
- To create a centralized resource for exploring transcriptomic information across cell types, species, and studies.
Main Methods:
- Updated the single cell Eye in a Disk (scEiaD) database content and structure.
- Developed the PLAE (https://plae.nei.nih.gov) web application for data visualization and exploration.
Main Results:
- The PLAE portal visualizes over a million cells from vertebrate eye and body transcriptomes.
- Data spans four species, 60 cell types, six ocular tissues, and 23 body tissues from 35 publications.
- Successfully replicated known markers and identified novel cone human region markers.
Conclusions:
- The PLAE web application provides a powerful tool for the eye research community.
- Enables hypothesis testing on a diverse, community-derived gene expression database.
- Facilitates research into gene expression patterns across ocular and body cell types.
