University of Massachusetts Medical School Faculty Publications
UMMS Affiliation
Program in Systems Biology; Program in Molecular Medicine; Graduate School of Biomedical Sciences
Publication Date
2020-12-23
Document Type
Article Preprint
Disciplines
Biochemical Phenomena, Metabolism, and Nutrition | Cellular and Molecular Physiology | Genetics and Genomics | Physiological Processes | Systems and Integrative Physiology
Abstract
In our group, we aim to understand metabolism in the nematode Caenorhabditis elegans and its relationships with gene expression, physiology and the response to therapeutic drugs. On March 15, 2020, a stay-at-home order was put into effect in the state of Massachusetts, USA, to flatten the curve of the spread of the novel SARS-CoV2 virus that causes COVID-19. For biomedical researchers in our state, this meant putting a hold on experiments for nine weeks until May 18, 2020. To keep the lab engaged and productive, and to enhance communication and collaboration, we embarked on an in-lab project that we all found important but that we never had the time for: the detailed annotation and drawing of C. elegans metabolic pathways. As a result, we present WormPaths, which is composed of two parts: 1) the careful manual annotation of metabolic genes into pathways, categories and levels, and 2) 66 pathway maps that include metabolites, metabolite structures, genes, reactions, and pathway connections between maps. These maps are available on our WormFlux website. We show that WormPaths provides easy-to-navigate maps and that the different levels in WormPaths can be used for metabolic pathway enrichment analysis of transcriptomic data. In the unfortunate event of additional lockdowns, we envision further developing these maps to be more interactive, with an analogy of road maps that are available on mobile devices.
Keywords
Genetics, metabolism, metabolic pathways, Caenorhabditis elegans, WormPaths
Rights and Permissions
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
DOI of Published Version
10.1101/2020.12.22.424026
Source
bioRxiv 2020.12.22.424026; doi: https://doi.org/10.1101/2020.12.22.424026. Link to preprint on bioRxiv.
Journal/Book/Conference Title
bioRxiv
Repository Citation
Walker MD, Giese GE, Holdorf AD, Bhattacharya S, Diot C, Garcia-Gonzalez A, Horowitz B, Lee Y, Leland T, Li X, Mirza Z, Na H, Nanda S, Ponomarova O, Zhang H, Zhang J, Yilmaz LS, Walhout AJ. (2020). WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization [preprint]. University of Massachusetts Medical School Faculty Publications. https://doi.org/10.1101/2020.12.22.424026. Retrieved from https://escholarship.umassmed.edu/faculty_pubs/1869
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License
Included in
Biochemical Phenomena, Metabolism, and Nutrition Commons, Cellular and Molecular Physiology Commons, Genetics and Genomics Commons, Physiological Processes Commons, Systems and Integrative Physiology Commons
Comments
This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.