SMPDB

SMPDB provides a curated collection of over 350 human small-molecule pathway diagrams, including metabolic, metabolic disease, metabolite signaling, and drug-action pathways, to support pathway interpretation and integration with metabolomics, proteomics, transcriptomics, and drug data, with more than two-thirds of pathways unique to SMPDB.

Key Features:

• Coverage: Contains over 350 distinct human small-molecule pathways, with more than two-thirds unique to SMPDB.
• Pathway Types: Includes human metabolic pathways, metabolic disease pathways, metabolite signaling pathways, and drug-action pathways.
• Diagram Annotation: Provides detailed, hyperlinked pathway diagrams annotated with organs, organelles, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures, and protein quaternary structures.
• Cross-database Links: Small molecules link to the Human Metabolome Database (HMDB) or DrugBank, and proteins or enzyme complexes link to UniProt entries.
• Search and Identifier Support: Supports queries by metabolite names, drug names, gene/protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs, and Agilent microarray IDs, returning matching pathways.
• Diagram Highlighting: Query results highlight corresponding molecules within pathway diagrams.
• Mapping Interface: Includes a mapping interface for visualizing gene, metabolite, and protein concentration data on pathways.
• Downloadable Data: Provides downloadable images, image maps, pathway descriptions, and tables.

Scientific Applications:

• Clinical metabolomics: Interpretation of metabolite patterns and biomarker-related pathway context.
• Transcriptomics and proteomics integration: Mapping gene and protein expression data onto pathways for functional interpretation.
• Systems biology: Integration of multi-omics concentration data with pathway representations for network-level analyses.
• Drug mechanism analysis: Examination of drug-action pathways and their metabolic impacts.
• Metabolic disease analysis: Investigation of disease-associated pathway alterations and related biochemical context.

Methodology:

Searches by metabolite, drug, gene/protein names or identifiers return matching pathways and highlight corresponding molecules; pathway diagram elements are hyperlinked to the Human Metabolome Database (HMDB), DrugBank, and UniProt; a mapping interface visualizes gene, metabolite, and protein concentration data.