IQuery

IQuery performs network- and pathway-based gene set analysis by querying pathways and networks from the Network Data Exchange (NDEx) to interpret biological processes.

Key Features:

• NDEx integration: Queries and analyzes pathways and networks stored in the Network Data Exchange (NDEx).
• Integration with diverse pathway sources: Incorporates curated pathways from WikiPathways and SIGNOR and published pathway figures spanning the last 27 years.
• Machine-assembled networks (INDRA): Generates machine-assembled networks using the INDRA system.
• NCI-PID v2.0 inclusion: Includes the NCI Pathway Interaction Database v2.0 for pathway interaction data.
• MSigDB and cBioPortal linkage: Links pathway analysis results with MSigDB (Molecular Signatures Database) and cBioPortal resources.
• Cytoscape compatibility: Provides network data compatible with Cytoscape for network visualization and manipulation.
• Data sharing: Supports storage and sharing of analysis results to enable result dissemination and reproducibility.
• Multi-method gene set analysis: Performs multiple gene set analysis methods against the aggregated pathway and network resources.

Scientific Applications:

• Hypothesis generation: Identifies active or modulated biological processes in specific experimental contexts.
• Pathway-context interpretation: Interprets gene sets within pathway and network contexts for genomics and systems biology studies.
• Translational research and personalized medicine: Supports analyses relevant to personalized medicine by linking gene sets to pathway alterations and cancer data via cBioPortal.

Methodology:

Implemented as a web application in JavaScript and Java; performs multiple gene set analyses using pathways and networks stored in NDEx and generates machine-assembled networks via INDRA.