GeneSigDB

GeneSigDB provides a curated, standardized repository of published gene expression signatures to enable comparative analysis and gene set enrichment across biological phenotypes.

Key Features:

• Manual Curation: Gene signatures are manually transcribed from published studies to capture reported gene lists accurately.
• Standardization: Signatures are standardized by mapping genes to the genome using EnsEMBL gene identifiers.
• Traceability: Each signature includes a traceable gene mapping history documenting the transformation from original data tables to standardized gene lists.
• Content Scope: Content initially emphasized cancer and stem cell signatures and has expanded to include immune cells, development, and lung disease.
• File Formats: Gene signatures are provided in .gmt and R/Bioconductor data file formats.
• Analytical Features: Supports identification of significant gene overlaps and generation of heatmap visualizations for comparative analyses.

Scientific Applications:

• Comparative Analysis: Compare experimental gene lists with published signatures to validate findings or identify shared patterns.
• Gene Set Enrichment Analysis (GSEA): Provision of .gmt files enables application of GSEA to identify enriched pathways and processes.
• Predictive Modeling: Curated signatures can be used as feature sets for developing predictive models for disease prognosis or diagnosis.

Methodology:

Manual transcription of gene signatures from publications; mapping of genes to the genome using EnsEMBL gene identifiers; recording of traceable gene mapping histories documenting transformation from original data tables to standardized gene lists; identification of significant gene overlaps; and generation of heatmap visualizations.