Altered Pathway Analyzer

Altered Pathway Analyzer identifies significantly rewired biological pathways in case–control gene expression datasets by analyzing changes in gene co-expression network topology.

Key Features:

• Gene Network Rewiring Detection: Detects alterations in gene connections within co-expression networks and associated regulatory frameworks.
• Pathway Prioritization: Prioritizes pathways altered between case and control conditions, including those influenced by transcription factors (TFs).
• Context-Specific Gene Enrichment: Reprioritizes pathways enriched with context-specific genes to improve biological interpretation.
• Cross-Dataset Pathway Analysis: Analyzes human gene expression datasets annotated with Entrez Gene IDs to identify altered pathways.

Scientific Applications:

• Disease Mechanism Investigation: Identifies pathways altered in disease conditions such as cancer using gene expression datasets.
• Gene Network Analysis: Examines changes in gene co-expression networks to detect regulatory and pathway perturbations.
• Functional Genomics Studies: Reveals biological processes affected by transcriptional network rewiring.

Methodology:

Altered Pathway Analyzer constructs gene co-expression networks from gene expression datasets with Entrez Gene IDs, quantifies changes in subnetwork topology between case and control conditions, and prioritizes pathways enriched with context-specific genes and transcription factor–associated regulation.