gCMAPWeb

gCMAPWeb constructs and queries connectivity maps to identify connections between disease phenotypes and drug effects by analyzing differential gene expression resulting from chemical and genetic perturbations.

Key Features:

• Integration with gCMAP: Interfaces with the gCMAP package to perform connectivity map construction and querying.
• Connectivity map construction: Builds and queries connectivity maps to relate differential gene expression signatures across perturbations.
• Data processing and standardization: Processes and standardizes microarray and RNAseq differential gene expression datasets.
• Gene set enrichment methods: Interrogates results using established gene set enrichment methods.
• User-defined data sources: Supports analysis of user-provided collections of differential gene expression data.
• Reference dataset generation: Provides capability to generate reference datasets from public repositories.

Scientific Applications:

• Discovery of disease–drug connections: Identifies commonalities between disease phenotypes and drug effects by comparing differential gene expression patterns.
• Therapeutic candidate and target identification: Facilitates nomination of potential therapeutic compounds and molecular targets from connectivity relationships.
• Mechanistic analysis of perturbations: Enables analysis of molecular mechanisms underlying chemical and genetic perturbations through expression signature comparison and enrichment analysis.

Methodology:

Processes user-defined collections of microarray and RNAseq differential gene expression data through standardized pipelines, applies established gene set enrichment methods, constructs and queries connectivity maps, and generates reference datasets from public repositories.