{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T14:58:07Z","timestamp":1774969087181,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T00:00:00Z","timestamp":1697500800000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"JSPS KAKENHI","award":["19K18321"],"award-info":[{"award-number":["19K18321"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,10,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The Kyoto Encyclopedia of Genes and Genomes (KEGG) database serves as a valuable systems biology resource and is widely utilized in diverse research fields. However, existing software does not allow flexible visualization and network analyses of the vast and complex KEGG data. We developed ggkegg, an R package that integrates KEGG information with ggplot2 and ggraph. ggkegg enables enhanced visualization and network analyses of KEGG data. We demonstrate the utility of the package by providing examples of its application in single-cell, bulk transcriptome, and microbiome analyses. ggkegg may empower researchers to analyze complex biological networks and present their results effectively.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The package and user documentation are available at: https:\/\/github.com\/noriakis\/ggkegg.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad622","type":"journal-article","created":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T11:29:27Z","timestamp":1697542167000},"source":"Crossref","is-referenced-by-count":21,"title":["<i>ggkegg<\/i>: analysis and visualization of KEGG data utilizing the grammar of graphics"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7721-9359","authenticated-orcid":false,"given":"Noriaki","family":"Sato","sequence":"first","affiliation":[{"name":"Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo , 4-6-1 Shirokanedai , Minato-ku, Tokyo 108-8639, Japan"}]},{"given":"Miho","family":"Uematsu","sequence":"additional","affiliation":[{"name":"Department of Immunology and Genomics, Graduate School of Medicine, Osaka Metropolitan University , Osaka 545-8585, Japan"},{"name":"Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo , Tokyo 108-8639, Japan"}]},{"given":"Kosuke","family":"Fujimoto","sequence":"additional","affiliation":[{"name":"Department of Immunology and Genomics, Graduate School of Medicine, Osaka Metropolitan University , Osaka 545-8585, Japan"},{"name":"Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo , Tokyo 108-8639, Japan"}]},{"given":"Satoshi","family":"Uematsu","sequence":"additional","affiliation":[{"name":"Department of Immunology and Genomics, Graduate School of Medicine, Osaka Metropolitan University , Osaka 545-8585, Japan"},{"name":"Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo , Tokyo 108-8639, Japan"}]},{"given":"Seiya","family":"Imoto","sequence":"additional","affiliation":[{"name":"Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo , 4-6-1 Shirokanedai , Minato-ku, Tokyo 108-8639, Japan"}]}],"member":"286","published-online":{"date-parts":[[2023,10,16]]},"reference":[{"key":"2023102913434893900_btad622-B1","doi-asserted-by":"crossref","first-page":"e00903","DOI":"10.1128\/mBio.00903-16","article-title":"JC polyomavirus infection of primary human renal epithelial cells is controlled by a type I IFN-induced response","volume":"7","author":"Assetta","year":"2016","journal-title":"mBio"},{"key":"2023102913434893900_btad622-B2","doi-asserted-by":"crossref","first-page":"2439","DOI":"10.1136\/gutjnl-2021-325021","article-title":"Cigarette smoke promotes colorectal cancer through modulation of gut microbiota and related metabolites","volume":"71","author":"Bai","year":"2022","journal-title":"Gut"},{"key":"2023102913434893900_btad622-B3","doi-asserted-by":"crossref","first-page":"2139","DOI":"10.1038\/s41388-022-02235-8","article-title":"Induction of APOBEC3-mediated genomic damage in urothelium implicates BK polyomavirus (BKPyV) as a hit-and-run driver for bladder cancer","volume":"41","author":"Baker","year":"2022","journal-title":"Oncogene"},{"key":"2023102913434893900_btad622-B4","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Cs\u00e1rdi","year":"2006","journal-title":"Int J Complex Syst"},{"key":"2023102913434893900_btad622-B5","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The NF-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2023102913434893900_btad622-B6","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.gpb.2022.04.008","article-title":"simplifyEnrichment: a Bioconductor package for clustering and visualizing functional enrichment results","volume":"21","author":"Gu","year":"2023","journal-title":"Genomics Proteomics Bioinf"},{"key":"2023102913434893900_btad622-B7","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","article-title":"Complex heatmaps reveal patterns and correlations in multidimensional genomic data","volume":"32","author":"Gu","year":"2016","journal-title":"Bioinformatics"},{"key":"2023102913434893900_btad622-B8","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"2023102913434893900_btad622-B9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/gix050","article-title":"Two distinct metacommunities characterize the gut microbiota in Crohn\u2019s disease patients","volume":"6","author":"He","year":"2017","journal-title":"Gigascience"},{"key":"2023102913434893900_btad622-B10","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023102913434893900_btad622-B11","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1002\/pro.4172","article-title":"KEGG mapping tools for uncovering hidden features in biological data","volume":"31","author":"Kanehisa","year":"2022","journal-title":"Protein Sci"},{"key":"2023102913434893900_btad622-B12","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023102913434893900_btad622-B13","doi-asserted-by":"crossref","first-page":"1830","DOI":"10.1093\/bioinformatics\/btt285","article-title":"Pathview: an R\/Bioconductor package for pathway-based data integration and visualization","volume":"29","author":"Luo","year":"2013","journal-title":"Bioinformatics"},{"key":"2023102913434893900_btad622-B14","doi-asserted-by":"crossref","first-page":"1612","DOI":"10.1101\/gr.201863.115","article-title":"An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography","volume":"26","author":"Nayfach","year":"2016","journal-title":"Genome Res"},{"key":"2023102913434893900_btad622-B15","author":"Pedersen","year":"2022"},{"key":"2023102913434893900_btad622-B16","author":"Pedersen","year":"2023"},{"key":"2023102913434893900_btad622-B17","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/1471-2105-13-20","article-title":"Graphite \u2013 a Bioconductor package to convert pathway topology to gene network","volume":"13","author":"Sales","year":"2012","journal-title":"BMC Bioinf"},{"key":"2023102913434893900_btad622-B18","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"2023102913434893900_btad622-B19","first-page":"100141","article-title":"clusterProfiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation (Camb)"},{"key":"2023102913434893900_btad622-B20","author":"Yu","year":"2023"},{"key":"2023102913434893900_btad622-B21","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1093\/bioinformatics\/btp167","article-title":"KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor","volume":"25","author":"Zhang","year":"2009","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad622\/52188118\/btad622.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/10\/btad622\/52673508\/btad622.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/10\/btad622\/52673508\/btad622.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,29]],"date-time":"2023-10-29T14:10:05Z","timestamp":1698588605000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad622\/7319364"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2023,10,1]]},"references-count":21,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2023,10,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad622","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,10,1]]},"published":{"date-parts":[[2023,10,1]]},"article-number":"btad622"}}