UMMS Affiliation
Program in Systems Biology; Program in Molecular Medicine; Graduate School of Biomedical Sciences
Publication Date
2021-06-12
Document Type
Article
Disciplines
Biochemical Phenomena, Metabolism, and Nutrition | Cellular and Molecular Physiology | Computational Biology
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. Visualization of the metabolic pathways that comprise the metabolic network is extremely useful for interpreting a wide variety of experiments. Detailed annotated metabolic pathway maps for C. elegans is mostly limited to pan-organismal maps, many with incomplete or inaccurate pathway and enzyme annotations. Here we present WormPaths, which is composed of two parts: 1) the careful manual annotation of metabolic genes into pathways, categories and levels, and 2) 62 pathway maps that include metabolites, metabolite structures, genes, reactions, and pathway connections between maps. These maps are available on the 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 future we envision further developing these maps to be more interactive, with an analogy of road maps that are available on mobile devices.
Keywords
C. elegans, metabolic pathways, metabolism, pathway enrichment analysis, pathway visualization
Rights and Permissions
© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
DOI of Published Version
10.1093/genetics/iyab089
Source
Walker MD, Giese GE, Holdorf AD, Bhattacharya S, Diot C, García-González AP, Horowitz BB, Lee YU, Leland T, Li X, Mirza Z, Na H, Nanda S, Ponomarova O, Zhang H, Zhang J, Yilmaz LS, Walhout AJM. WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization. Genetics. 2021 Jun 12:iyab089. doi: 10.1093/genetics/iyab089. Epub ahead of print. PMID: 34117752. Link to article on publisher's site
Journal/Book/Conference Title
Genetics
Related Resources
PubMed ID
34117752
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. (2021). WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization. Open Access Publications by UMass Chan Authors. https://doi.org/10.1093/genetics/iyab089. Retrieved from https://escholarship.umassmed.edu/oapubs/4783
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Biochemical Phenomena, Metabolism, and Nutrition Commons, Cellular and Molecular Physiology Commons, Computational Biology Commons
Comments
This article is based on a previously available preprint in bioRxiv.