From 20th century metabolic wall charts to 21st century systems biology: database of mammalian metabolic enzymes

The organization of the mammalian genome into gene subsets corresponding to specific functional classes has provided key tools for systems biology research. Here, we have created a web-accessible resource called the https://hpcwebapps.cit.nih.gov/ESBL/Database/MetabolicEnzymes/MetabolicEnzymeDatabas...

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Bibliographic Details
Published in:American journal of physiology. Renal physiology 2017-03, Vol.312 (3), p.F533-F542
Main Authors: Corcoran, Callan C, Grady, Cameron R, Pisitkun, Trairak, Parulekar, Jaya, Knepper, Mark A
Format: Article
Language:English
Subjects:
Animals
Audiovisual Aids
Data Mining
Databases, Protein
Diffusion of Innovation
Energy Metabolism
Enzymes - genetics
Enzymes - metabolism
Gene Expression Regulation, Enzymologic
Kidney Tubules - enzymology
Mice
Protein Interaction Maps
Rats
RNA, Messenger - genetics
RNA, Messenger - metabolism
Systems Biology - methods
Vasopressins - metabolism
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Summary:The organization of the mammalian genome into gene subsets corresponding to specific functional classes has provided key tools for systems biology research. Here, we have created a web-accessible resource called the https://hpcwebapps.cit.nih.gov/ESBL/Database/MetabolicEnzymes/MetabolicEnzymeDatabase.html) keyed to the biochemical reactions represented on iconic metabolic pathway wall charts created in the previous century. Overall, we have mapped 1,647 genes to these pathways, representing ~7 percent of the protein-coding genome. To illustrate the use of the database, we apply it to the area of kidney physiology. In so doing, we have created an additional database ( https://hpcwebapps.cit.nih.gov/ESBL/Database/MetabolicEnzymes/), mapping mRNA abundance measurements (mined from RNA-Seq studies) for all metabolic enzymes to each of 14 renal tubule segments. We carry out bioinformatics analysis of the enzyme expression pattern among renal tubule segments and mine various data sources to identify vasopressin-regulated metabolic enzymes in the renal collecting duct.
ISSN:1931-857X
1522-1466
DOI:10.1152/ajprenal.00601.2016