Atlas of metabolism regulation diagrams: post-translational modification of enzymes#

Authors#

Hanna Borlinghaus, Irina-Afrodita Balaur, Adrien Rougny, Michael Blinov, Marek Ostaszewski, Nikolaus Berndt, Antonio Fabregat, Tatiana Serebriyskaya, Valeriya Berzhitskaya, Vasundra Touré, Olga Ivanova, Marcio Luis Acencio, Luiz Ladeira, Alexander Kuritsyn, James Greene, John Albanese, Maria Del Carmen Heredia, Frank T. Bergmann, Piotr Gawron, Ahmed Hemedan, Anatoly Sorokin, Hongwu Ma, Igor Goryanin, Venkata Pardhasaradhi Satagopam, Ines Thiele, Falk Schreiber, Charles Auffray, Reinhard Schneider, Alexander Mazein

Abstract#

The advances in comprehensive reconstructions of the human metabolic network and signalling pathways make it possible to better understand the regulation of human metabolism. At the same time, the information is scattered among various resources, and there is no reference resource specifically dedicated to metabolism regulation pathways. We offer a method to systematically identify connections between metabolic and signalling networks with the focus on the regulation of metabolic enzymes by merging Reactome Neo4j and Recon2Neo4j resources. We present a collection of diagrams available in the MINERVA platform for online access and exploration. The diagrams are built in the freely available yEd Graph Editor, converted to the SBGN Process Description standard format. The resource includes the regulation of such metabolic pathways as glucose metabolism, cholesterol metabolism, eNOS pathway, synthesis of important molecules like estrogens, eicosanoids and nitric oxide synthases, NF-kB-PKCe axis in lung cancer cells and the mechanism of action of aspirin. The resource provides an easy overview of metabolism regulation pathways for learning purposes and for supporting research projects, as well as the methodology for further exploration of the interplay between metabolic and signalling networks in the context of metabolism regulation and related diseases.

Availability#

All the maps and the lists of identified connections between signalling and metabolic networks are available at https://metabolismregulation.github.io and accessible for browsing via the MINERVA platform. The map diagrams and the corresponding data files are distributed under the terms of the Creative Commons Public Domain (CC0) License.