PCMDB

PCMDB provides a curated database of plant cell marker genes to support cell-type identification and analysis in plant single-cell transcriptomic and genomic studies.

Key Features:

• Extensive Data Collection: Contains 81,117 cell marker genes across 263 cell types and 22 tissues in six plant species, compiled from over 130,000 research publications.
• Uniform Annotation Pipeline: Applies a standardized annotation pipeline to ensure consistency and reliability of annotations.
• Visualization Tools: Includes eFP Browser, bar plots, and UMAP/TSNE graphs for visualizing tissue- and cell-specific expression patterns.
• Analysis Tools: Supports SCSA (Single Cell Signature Analysis) and SingleR for gene-expression-based cell-type annotation.
• Search Functionality: Provides five built-in search engines for targeted retrieval of marker data.
• Homology-Based Marker Prediction: Enables identification of candidate marker genes in unsupported plant species via homologous searches against markers from supported species.
• Manual Curation: Marker entries and annotations were compiled through manual curation of the literature.

Scientific Applications:

• Cell Type Annotation: Facilitates annotation of cell types in single-cell datasets using curated marker genes and SCSA/SingleR.
• Tissue-Specific Expression Analysis: Supports analysis of tissue- and cell-specific gene expression patterns across 22 tissues.
• Cross-Species Marker Prediction: Enables prediction of candidate markers in other plant species through homology-based searches.
• Single-Cell and Genomic Study Support: Provides reference markers to aid interpretation of plant single-cell transcriptomic and genomic data.

Methodology:

Data processing used a standardized annotation pipeline; visualization employed eFP Browser, bar plots, and UMAP/TSNE; analysis and annotation used SCSA and SingleR; and homology-based searches were used for marker prediction.