{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T11:51:46Z","timestamp":1769860306562,"version":"3.49.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2017,12,21]],"date-time":"2017-12-21T00:00:00Z","timestamp":1513814400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Network inference provides a global view of the relations existing between gene expression in a given transcriptomic experiment (often only for a restricted list of chosen genes). However, it is still a challenging problem: even if the cost of sequencing techniques has decreased over the last years, the number of samples in a given experiment is still (very) small compared to the number of genes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We propose a method to increase the reliability of the inference when RNA-seq expression data have been measured together with an auxiliary dataset that can provide external information on gene expression similarity between samples. Our statistical approach, hd-MI, is based on imputation for samples without available RNA-seq data that are considered as missing data but are observed on the secondary dataset. hd-MI can improve the reliability of the inference for missing rates up to 30% and provides more stable networks with a smaller number of false positive edges. On a biological point of view, hd-MI was also found relevant to infer networks from RNA-seq data acquired in adipose tissue during a nutritional intervention in obese individuals. In these networks, novel links between genes were highlighted, as well as an improved comparability between the two steps of the nutritional intervention.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Software and sample data are available as an R package, RNAseqNet, that can be downloaded from the Comprehensive R Archive Network (CRAN).<\/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\/btx819","type":"journal-article","created":{"date-parts":[[2017,12,20]],"date-time":"2017-12-20T22:03:02Z","timestamp":1513807382000},"page":"1726-1732","source":"Crossref","is-referenced-by-count":7,"title":["Multiple hot-deck imputation for network inference from RNA sequencing data"],"prefix":"10.1093","volume":"34","author":[{"given":"Alyssa","family":"Imbert","sequence":"first","affiliation":[{"name":"MIAT, Universit\u00e9 de Toulouse, INRA, F-31326 Castanet-Tolosan, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Armand","family":"Valsesia","sequence":"additional","affiliation":[{"name":"Nestl\u00e9 Institute of Health Sciences, CH-1015 Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caroline","family":"Le Gall","sequence":"additional","affiliation":[{"name":"Methodomics, F-31200 Toulouse, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudia","family":"Armenise","sequence":"additional","affiliation":[{"name":"Quartzbio, CH-1202 Geneva, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gregory","family":"Lefebvre","sequence":"additional","affiliation":[{"name":"Nestl\u00e9 Institute of Health Sciences, CH-1015 Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre-Antoine","family":"Gourraud","sequence":"additional","affiliation":[{"name":"Methodomics, F-31200 Toulouse, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathalie","family":"Viguerie","sequence":"additional","affiliation":[{"name":"UMR1048, Obesity Research Laboratory, Institute of Metabolic and Cardiovascular Diseases (I2MC), Inserm, Toulouse, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathalie","family":"Villa-Vialaneix","sequence":"additional","affiliation":[{"name":"MIAT, Universit\u00e9 de Toulouse, INRA, F-31326 Castanet-Tolosan, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,12,21]]},"reference":[{"key":"2023012713455876500_btx819-B1","author":"Allen","year":"2012"},{"key":"2023012713455876500_btx819-B2","volume-title":"Verification of Methods for Gene Network Inference from Systems Genetics Data","author":"Allouche","year":"2013"},{"key":"2023012713455876500_btx819-B3","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1111\/j.1751-5823.2010.00103.x","article-title":"A review of hot deck imputation for survey non-response","volume":"78","author":"Andridge","year":"2010","journal-title":"Int. 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