WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization
AuthorsWalker, Melissa D.
Giese, Gabrielle E.
Holdorf, Amy D.
Yilmaz, L. Safak
Walhout, Albertha J. M.
UMass Chan AffiliationsGraduate School of Biomedical Sciences
Program in Molecular Medicine
Program in Systems Biology
Document TypeJournal Article
pathway enrichment analysis
Biochemical Phenomena, Metabolism, and Nutrition
Cellular and Molecular Physiology
MetadataShow full item record
AbstractIn 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.
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
Permanent Link to this Itemhttp://hdl.handle.net/20.500.14038/41980
This article is based on a previously available preprint in bioRxiv.