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

Comments

This article is based on a previously available preprint in bioRxiv.

Related Resources

Link to Article in PubMed

PubMed ID

34117752

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

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