OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization

Comput Struct Biotechnol J. 2022 May 10:20:2280-2291. doi: 10.1016/j.csbj.2022.05.006. eCollection 2022.


OncoboxPD (Oncobox pathway databank) available at https://open.oncobox.com is the collection of 51 672 uniformly processed human molecular pathways. Superposition of all pathways formed interactome graph of protein-protein interactions and metabolic reactions containing 361 654 interactions and 64 095 molecular participants. Pathways are uniformly classified by biological processes, and each pathway node is algorithmically functionally annotated by specific activator/repressor role. This enables online calculation of statistically supported pathway activation levels (PALs) with the built-in bioinformatic tool using custom RNA/protein expression profiles. Each pathway can be visualized as static or dynamic graph, where vertices are molecules participating in a pathway and edges are interactions or reactions between them. Differentially expressed nodes in a pathway can be visualized in two-color mode with user-defined color scale. For every comparison, OncoboxPD also generates a graph summarizing top up- and downregulated pathways.

Keywords: ARR, activation/repressor role coefficient; BEL, Biological Expression Language; Interactomics; KEGG, Kyoto Encyclopedia of Genes and Genomes; Metabolomics; Molecular pathway database; PAL, pathway activation level; Pathway activation level; Pathway visualization; Protein–protein interactions; SPIKE, Signaling Pathways Integrated Knowledge Engine; SPOKE, Scalable Precision Medicine Open Knowledge Engine; VM, virtual machine.

Associated data

  • figshare/10.6084/m9.figshare.16617676.)