PPMdb

PPMdb catalogs pathway-based gene and microsatellite markers across plant genomes to enable pathway-centric identification and mapping of genes and microsatellites for genetic and functional analysis.

Key Features:

• Pathway Gene Set Mining Approach: Introduces a pathway gene set mining approach to develop two classes of annotation-based markers, Pathway Gene-Targeted Markers (PGTMs) and Pathway Microsatellite-Targeted Markers (PMTMs).
• Pathway Gene-Targeted Markers (PGTMs): Markers that target genes controlling specific pathways or biological processes.
• Pathway Microsatellite-Targeted Markers (PMTMs): Markers that target microsatellites located within pathway-specific gene regions.
• Extensive Marker Database: Contains 2,690,742 pathway-based markers across 82 plant genomes, comprising 691,555 PGTMs and 1,999,187 PMTMs.
• Enzyme-Coding Gene Mapping: Maps 165,378 enzyme-coding genes against 126 KEGG (Kyoto Encyclopedia of Genes and Genomes) reference pathway maps.
• Visualization and Genome Mapping Tools: Includes Map Browse for visualizing markers on KEGG pathway maps, JBrowse for mapping markers across genomes, and Species Comparison for comparing marker panels between species.

Scientific Applications:

• Pathway-targeted gene identification: Enables identification of genes associated with specific KEGG pathways.
• Trait-associated variation and characterization: Supports exploration of genetic variation linked to desired traits and trait characterization in plant research.

Methodology:

Applied a pathway gene set mining approach to generate PGTMs and PMTMs; mapped 165,378 enzyme-coding genes to 126 KEGG pathway maps; compiled 2,690,742 markers across 82 plant genomes; visualized markers on KEGG maps and mapped markers across genomes via Map Browse and JBrowse.