{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T02:07:18Z","timestamp":1772244438689,"version":"3.50.1"},"reference-count":23,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T00:00:00Z","timestamp":1725926400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>We present a tool for multi-omics data analysis that enables simultaneous visualization of up to four types of omics data on organism-scale metabolic network diagrams. The tool\u2019s interactive web-based metabolic charts depict the metabolic reactions, pathways, and metabolites of a single organism as described in a metabolic pathway database for that organism; the charts are constructed using automated graphical layout algorithms. The multi-omics visualization facility paints each individual omics dataset onto a different \u201cvisual channel\u201d of the metabolic-network diagram. For example, a transcriptomics dataset might be displayed by coloring the reaction arrows within the metabolic chart, while a companion proteomics dataset is displayed as reaction arrow thicknesses, and a complementary metabolomics dataset is displayed as metabolite node colors. Once the network diagrams are painted with omics data, semantic zooming provides more details within the diagram as the user zooms in. Datasets containing multiple time points can be displayed in an animated fashion. The tool will also graph data values for individual reactions or metabolites designated by the user. The user can interactively adjust the mapping from data value ranges to the displayed colors and thicknesses to provide more informative diagrams.<\/jats:p>","DOI":"10.3389\/fbinf.2024.1395981","type":"journal-article","created":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T01:13:34Z","timestamp":1725930814000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Visual analysis of multi-omics data"],"prefix":"10.3389","volume":"4","author":[{"given":"Austin","family":"Swart","sequence":"first","affiliation":[]},{"given":"Ron","family":"Caspi","sequence":"additional","affiliation":[]},{"given":"Suzanne","family":"Paley","sequence":"additional","affiliation":[]},{"given":"Peter D.","family":"Karp","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2024,9,10]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"4180","DOI":"10.1128\/aem.00256-16","article-title":"Culturing synechocystis sp. strain pc 6803 with n2 and co2 in a diel regime reveals multiphase glycogen dynamics with low maintenance costs","volume":"82","author":"Angermayr","year":"2016","journal-title":"Appl. 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