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dc.contributor.authorWalker, Melissa D.
dc.contributor.authorGiese, Gabrielle E.
dc.contributor.authorHoldorf, Amy D.
dc.contributor.authorBhattacharya, Sushila
dc.contributor.authorDiot, Cedric
dc.contributor.authorGarcia-Gonzalez, Aurian
dc.contributor.authorHorowitz, Brent
dc.contributor.authorLee, Yong-Uk
dc.contributor.authorLeland, Thomas
dc.contributor.authorLi, Xuhang
dc.contributor.authorMirza, Zeynep
dc.contributor.authorNa, Huimin
dc.contributor.authorNanda, Shivani
dc.contributor.authorPonomarova, Olga
dc.contributor.authorZhang, Hefei
dc.contributor.authorZhang, Jingyan
dc.contributor.authorYilmaz, L. Safak
dc.contributor.authorWalhout, Albertha J. M.
dc.date2022-08-11T08:10:00.000
dc.date.accessioned2022-08-23T16:52:04Z
dc.date.available2022-08-23T16:52:04Z
dc.date.issued2021-06-12
dc.date.submitted2021-10-27
dc.identifier.citation<p>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. <a href="https://doi.org/10.1093/genetics/iyab089">Link to article on publisher's site</a></p>
dc.identifier.issn0016-6731 (Linking)
dc.identifier.doi10.1093/genetics/iyab089
dc.identifier.pmid34117752
dc.identifier.urihttp://hdl.handle.net/20.500.14038/41980
dc.description<p>This article is based on a previously available preprint in <a href="https://doi.org/10.1101/2020.12.22.424026" target="_blank" title="view preprint in bioRxiv">bioRxiv</a>.</p>
dc.description.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.
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=34117752&dopt=Abstract">Link to Article in PubMed</a></p>
dc.rights© 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.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectC. elegans
dc.subjectmetabolic pathways
dc.subjectmetabolism
dc.subjectpathway enrichment analysis
dc.subjectpathway visualization
dc.subjectBiochemical Phenomena, Metabolism, and Nutrition
dc.subjectCellular and Molecular Physiology
dc.subjectComputational Biology
dc.titleWormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization
dc.typeJournal Article
dc.source.journaltitleGenetics
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=5816&amp;context=oapubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/oapubs/4783
dc.identifier.contextkey25625669
refterms.dateFOA2022-08-23T16:52:04Z
html.description.abstract<p>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.</p>
dc.identifier.submissionpathoapubs/4783
dc.contributor.departmentGraduate School of Biomedical Sciences
dc.contributor.departmentProgram in Molecular Medicine
dc.contributor.departmentProgram in Systems Biology


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© 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.
Except where otherwise noted, this item's license is described as © 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.