OncoboxPD

OncoboxPD provides a resource of 51,672 uniformly processed human molecular pathways and an interactome graph to quantify pathway activation via Pathway Activation Levels (PALs) calculated from custom RNA and protein expression profiles.

Key Features:

• Pathway collection: Contains 51,672 uniformly processed human molecular pathways.
• Interactome graph: Integrates protein-protein interactions and metabolic reactions comprising 361,654 interactions among 64,095 molecular participants and classifies pathways by biological processes.
• Node annotation: Annotates pathway nodes with activator or repressor roles.
• Pathway Activation Levels (PALs): Computes statistically supported PALs using custom RNA and protein expression profiles.
• Visualization: Renders pathways as static or dynamic graphs with vertices as molecules and edges as interactions, highlighting differentially expressed nodes in a two-color mode with a user-defined color scale.
• Comparative analysis: Generates summary graphs that identify top up- and downregulated pathways for differential expression and pathway dynamics analyses.

Scientific Applications:

• Differential expression studies: Identifies and summarizes top up- and downregulated pathways based on input expression data.
• Pathway dynamics analysis: Assesses pathway activity changes under experimental conditions using PALs and summary graphs.
• Oncology and molecular biology research: Supports pathway-level interpretation of RNA and protein expression data in cancer and molecular biology contexts.

Methodology:

Uniform processing of human molecular pathways; construction of an interactome graph integrating protein–protein interactions and metabolic reactions; annotation of nodes as activators or repressors; calculation of Pathway Activation Levels (PALs) from custom RNA/protein expression profiles; visualization of pathways as static or dynamic graphs with two-color highlighting of differentially expressed nodes; generation of summary graphs identifying top up- and downregulated pathways.