WhichGenes

WhichGenes manages creation, integration, manipulation, and export of gene sets to support gene set enrichment analysis and downstream functional genomics, pathway analysis, and systems biology applications.

Key Features:

• Gene set building: Supports specification and creation of new gene sets by extracting always-updated gene lists from multiple databases and unstructured biological data sources.
• Parallel query execution: Executes multiple queries concurrently to accelerate retrieval and assembling of gene sets.
• Set management and manipulation: Provides persistent storage and operations for editing, deleting, renaming, and generating new sets via intersection, union, and difference operators.
• Export capabilities: Exports gene sets in multiple output formats with selection among different gene identifiers.
• Programmatic access: Exposes functionality via a Representational State Transfer (REST) web service API for integration into automated pipelines.

Scientific Applications:

• Gene set enrichment analysis: Supplies curated and custom gene sets for use in enrichment workflows and statistical interpretation of gene lists.
• Functional genomics studies: Enables creation and comparison of gene sets for gene function and annotation analyses.
• Pathway analysis: Facilitates generation and export of pathway-related gene sets for pathway enrichment and mapping.
• Systems biology: Supports assembly and combination of gene sets for network-level and systems-level investigations.

Methodology:

Extraction of always-updated gene lists from multiple databases and unstructured biological data sources; concurrent query execution; set operations (intersection, union, difference); export to multiple output formats with selectable gene identifiers; and access via a REST web service API.