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

Autor:	Zolotovskaia MA; Omicsway Corp., Walnut, CA 91789, USA.; Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.; Pirogov Russian National Research Medical University, Moscow 117997, Russia., Tkachev VS; Omicsway Corp., Walnut, CA 91789, USA., Guryanova AA; Omicsway Corp., Walnut, CA 91789, USA.; I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia., Simonov AM; World-Class Research Center 'Digital biodesign and personalized healthcare', Sechenov First Moscow State Medical University, Moscow, Russia., Raevskiy MM; World-Class Research Center 'Digital biodesign and personalized healthcare', Sechenov First Moscow State Medical University, Moscow, Russia., Efimov VV; World-Class Research Center 'Digital biodesign and personalized healthcare', Sechenov First Moscow State Medical University, Moscow, Russia., Wang Y; Clinical Laboratory, Qingdao Central Hospital, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, China., Sekacheva MI; World-Class Research Center 'Digital biodesign and personalized healthcare', Sechenov First Moscow State Medical University, Moscow, Russia., Garazha AV; Omicsway Corp., Walnut, CA 91789, USA., Borisov NM; Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia., Kuzmin DV; Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia., Sorokin MI; Omicsway Corp., Walnut, CA 91789, USA.; Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.; I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia.; PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium., Buzdin AA; Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.; World-Class Research Center 'Digital biodesign and personalized healthcare', Sechenov First Moscow State Medical University, Moscow, Russia.; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.; PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium.
Jazyk:	angličtina
Zdroj:	Computational and structural biotechnology journal [Comput Struct Biotechnol J] 2022 May 10; Vol. 20, pp. 2280-2291. Date of Electronic Publication: 2022 May 10 (Print Publication: 2022).
DOI:	10.1016/j.csbj.2022.05.006
Abstrakt:	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. Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. MZ, VT, AGa, AGu, MSo have a financial relationship with Omicsway Corp. The remaining authors declare that they have no conflict of interest. (© 2022 The Authors.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu