Stem Cell Discovery Engine (SCDE)

Stem Cell Discovery Engine (SCDE) aggregates a curated repository of cancer and tissue stem cell experiments and integrates them with Galaxy-based analytical tools to enable systematic comparison of gene and pathway signatures across blood, intestine, and brain studies.

Key Features:

• Curated Database: Hosts 53 public studies comprising 1098 assays of tissue and cancer stem cell experiments from blood, intestine, and brain.
• ISA-Tab Format: Captures experimental metadata in the Investigation/Study/Assay (ISA-Tab) multi-omics format for standardized data representation.
• Galaxy Integration: Integrates with the Galaxy analytical framework and provides tools for gene list comparisons against GeneSigDB, MSigDB, and SCDE's curated experiments.
• Pathway Analysis: Links experimental results to WikiPathways to support pathway-level analyses across CSC datasets.

Scientific Applications:

• Comparative Signature Analysis: Enables systematic comparison of stem-like gene and pathway signatures across diverse experimental systems.
• Mechanistic Investigation: Supports studies of molecular mechanisms underlying cancer stem cell behavior in various cancers.
• Target Identification: Facilitates identification and prioritization of candidate therapeutic targets via gene and pathway-level comparisons.

Methodology:

Curates experimental data into ISA-Tab format, integrates datasets with the Galaxy analytical framework, performs gene list comparisons against GeneSigDB and MSigDB, and links results to WikiPathways for pathway analysis.