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

• Published in: Computational and structural biotechnology journal Vol. 20; pp. 2280 - 2291
• Main Authors: Zolotovskaia, Marianna A., Tkachev, Victor S., Guryanova, Anastasia A., Simonov, Alexander M., Raevskiy, Mikhail M., Efimov, Victor V., Wang, Ye, Sekacheva, Marina I., Garazha, Andrew V., Borisov, Nicolas M., Kuzmin, Denis V., Sorokin, Maxim I., Buzdin, Anton A.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.01.2022; Research Network of Computational and Structural Biotechnology; Elsevier
• Subjects: Data; Interactomics; Metabolomics; Molecular pathway database; Pathway activation level; Pathway visualization; Protein–protein interactions; Metabolomics; ARR; Protein–protein interactions; Molecular pathway database; Interactomics; BEL; Pathway visualization; SPIKE; VM; Pathway activation level; KEGG; PAL; SPOKE; BEL, Biological Expression Language; PAL, pathway activation level; VM, virtual machine; KEGG, Kyoto Encyclopedia of Genes and Genomes; ARR, activation/repressor role coefficient; SPOKE, Scalable Precision Medicine Open Knowledge Engine; SPIKE, Signaling Pathways Integrated Knowledge Engine
• ISSN: 2001-0370; 2001-0370
• DOI: 10.1016/j.csbj.2022.05.006

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.