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

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 0...

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Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9120235/
https://www.ncbi.nlm.nih.gov/pubmed/35615022
http://dx.doi.org/10.1016/j.csbj.2022.05.006
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author 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.
author_facet 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.
author_sort Zolotovskaia, Marianna A.
collection PubMed
description 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.
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spelling pubmed-91202352022-05-24 OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization 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. Comput Struct Biotechnol J Data Article 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. Research Network of Computational and Structural Biotechnology 2022-05-10 /pmc/articles/PMC9120235/ /pubmed/35615022 http://dx.doi.org/10.1016/j.csbj.2022.05.006 Text en © 2022 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Data Article
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.
OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization
title OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization
title_full OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization
title_fullStr OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization
title_full_unstemmed OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization
title_short OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization
title_sort oncoboxpd: human 51 672 molecular pathways database with tools for activity calculating and visualization
topic Data Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9120235/
https://www.ncbi.nlm.nih.gov/pubmed/35615022
http://dx.doi.org/10.1016/j.csbj.2022.05.006
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