{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T00:24:49Z","timestamp":1771460689286,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2018,7,13]],"date-time":"2018-07-13T00:00:00Z","timestamp":1531440000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"INSERM, AP-HP"},{"name":"Assistance Publique-H\u00f4pitaux de Paris"},{"name":"Bio-Psy Labex","award":["ANR-11-IDEX-0004-02"],"award-info":[{"award-number":["ANR-11-IDEX-0004-02"]}]},{"DOI":"10.13039\/100018375","name":"Fondation FondaMental","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100018375","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>RNA quantification experiments result in compositional data, however usual methods for compositional data analysis [additive log ratio (alr), centered log ratio (clr), isometric log ratio (ilr)] do not apply easily and give results difficult to interpret. To handle this, a method based on disjoint subgraphs in a graph whose nodes are the quantified RNAs is proposed. Edges in the graph are defined by lack of change in ratios of the corresponding RNAs between conditions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The methods is suited for qRT-PCR and RNA-Seq data analyses, and leads to easy-to-interpret, graphical results and the identification of set of genes that share a similar behavior when the studied condition changes. For qRT-PCR data, it has better statistical properties than the common \u0394\u0394Cq method.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Construction of all pairwise ratio analysis P-values matrix, and conversion into a graph was implemented in an R package, named SARP.compo. It is freely available for download on the CRAN repository. Example R script using the package are provided as Supplementary Material; the R package includes the data needed. One of these scripts reproduces the Figure\u00a02 of this paper.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty629","type":"journal-article","created":{"date-parts":[[2018,7,13]],"date-time":"2018-07-13T11:25:10Z","timestamp":1531481110000},"page":"258-265","source":"Crossref","is-referenced-by-count":11,"title":["Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8382-1493","authenticated-orcid":false,"given":"Emmanuel","family":"Curis","sequence":"first","affiliation":[{"name":"Laboratoire de Biomath\u00e9matiques, Facult\u00e9 de Pharmacie de Paris, Universit\u00e9 Paris Descartes, Sorbonne Paris Cit\u00e9, Paris F-75006, France"},{"name":"UMR S-1144 INSERM\u2014Universit\u00e9 Paris Descartes\u2014Universit\u00e9 Paris Diderot, Paris F-75006, France"},{"name":"Service de Bioinformatique et Information M\u00e9dicale, H\u00f4pital Saint-Louis, AP-HP, Paris F-75012, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cindie","family":"Courtin","sequence":"additional","affiliation":[{"name":"UMR S-1144 INSERM\u2014Universit\u00e9 Paris Descartes\u2014Universit\u00e9 Paris Diderot, Paris F-75006, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre Alexis","family":"Geoffroy","sequence":"additional","affiliation":[{"name":"UMR S-1144 INSERM\u2014Universit\u00e9 Paris Descartes\u2014Universit\u00e9 Paris Diderot, Paris F-75006, France"},{"name":"P\u00f4le de Psychiatrie et de M\u00e9decine, Addictologique GH Saint-Louis \u2013 Lariboisi\u00e8re \u2013 F. 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