{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:25:13Z","timestamp":1761488713768},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1937,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Studying the interplay between gene expression and metabolite levels can yield important information on the physiology of stress responses and adaptation strategies. Performing transcriptomics and metabolomics in parallel during time-series experiments represents a systematic way to gain such information. Several combined profiling datasets have been added to the public domain and they form a valuable resource for hypothesis generating studies. Unfortunately, detecting coresponses between transcript levels and metabolite abundances is non-trivial: they cannot be assumed to overlap directly with underlying biochemical pathways and they may be subject to time delays and obscured by considerable noise.<\/jats:p>\n               <jats:p>Results: Our aim was to predict pathway comemberships between metabolites and genes based on their coresponses to applied stress. We found that in the presence of strong noise and time-shifted responses, a hidden Markov model-based similarity outperforms the simpler Pearson correlation but performs comparably or worse in their absence. Therefore, we propose a supervised method that applies pathway information to summarize similarity statistics to a consensus statistic that is more informative than any of the single measures. Using four combined profiling datasets, we show that comembership between metabolites and genes can be predicted for numerous KEGG pathways; this opens opportunities for the detection of transcriptionally regulated pathways and novel metabolically related genes.<\/jats:p>\n               <jats:p>Availability: A command-line software tool is available at http:\/\/www.cin.ufpe.br\/~igcf\/Metabolites.<\/jats:p>\n               <jats:p>Contact: \u00a0henning@psc.riken.jp; igcf@cin.ufpe.br<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr231","type":"journal-article","created":{"date-parts":[[2011,6,17]],"date-time":"2011-06-17T23:32:32Z","timestamp":1308353552000},"page":"i357-i365","source":"Crossref","is-referenced-by-count":30,"title":["Detection and interpretation of metabolite\u2013transcript coresponses using combined profiling data"],"prefix":"10.1093","volume":"27","author":[{"given":"Henning","family":"Redestig","sequence":"first","affiliation":[{"name":"1 RIKEN Plant Science Center, Yokohama, Japan and 2Center of Informatics, Federal University of Pernambuco, Recife, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivan G.","family":"Costa","sequence":"additional","affiliation":[{"name":"1 RIKEN Plant Science Center, Yokohama, Japan and 2Center of Informatics, Federal University of Pernambuco, Recife, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,6,14]]},"reference":[{"key":"2023012512143553900_B1","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1126\/science.277.5330.1275","article-title":"A test case of correlation metric construction of a reaction Pathway from Measurements","volume":"277","author":"Arkin","year":"1997","journal-title":"Science"},{"key":"2023012512143553900_B2","doi-asserted-by":"crossref","first-page":"e1000270","DOI":"10.1371\/journal.pcbi.1000270","article-title":"Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae","volume":"5","author":"Bradley","year":"2009","journal-title":"PLoS Comput. 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