{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T17:35:32Z","timestamp":1732037732944},"reference-count":70,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2018,7,6]],"date-time":"2018-07-06T00:00:00Z","timestamp":1530835200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"French Ministry of Research and National Research Agency"},{"name":"French MetaboHUB","award":["ANR-INBS-0010"]},{"name":"European Commission\u2019s Horizon 2020","award":["654241"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,15]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Metabolomics has shown great potential to improve the understanding of complex diseases, potentially leading to therapeutic target identification. However, no single analytical method allows monitoring all metabolites in a sample, resulting in incomplete metabolic fingerprints. This incompleteness constitutes a stumbling block to interpretation, raising the need for methods that can enrich those fingerprints. We propose MetaboRank, a new solution inspired by social network recommendation systems for the identification of metabolites potentially related to a metabolic fingerprint.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n MetaboRank method had been used to enrich metabolomics data obtained on cerebrospinal fluid samples from patients suffering from hepatic encephalopathy (HE). MetaboRank successfully recommended metabolites not present in the original fingerprint. The quality of recommendations was evaluated by using literature automatic search, in order to check that recommended metabolites could be related to the disease. Complementary mass spectrometry experiments and raw data analysis were performed to confirm these suggestions. In particular, MetaboRank recommended the overlooked \u03b1-ketoglutaramate as a metabolite which should be added to the metabolic fingerprint of HE, thus suggesting that metabolic fingerprints enhancement can provide new insight on complex diseases.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n Method is implemented in the MetExplore server and is available at www.metexplore.fr. A tutorial is available at https:\/\/metexplore.toulouse.inra.fr\/com\/tutorials\/MetaboRank\/2017-MetaboRank.pdf.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty577","type":"journal-article","created":{"date-parts":[[2018,7,4]],"date-time":"2018-07-04T19:39:34Z","timestamp":1530733174000},"page":"274-283","source":"Crossref","is-referenced-by-count":28,"title":["MetaboRank: network-based recommendation system to interpret and enrich metabolomics results"],"prefix":"10.1093","volume":"35","author":[{"given":"Cl\u00e9ment","family":"Frainay","sequence":"first","affiliation":[{"name":"Toxalim, Universit\u00e9 de Toulouse, INRA, Universit\u00e9 de Toulouse 3 Paul Sabatier, Toulouse, France"}]},{"given":"Sandrine","family":"Aros","sequence":"additional","affiliation":[{"name":"Medday Pharmaceuticals, Paris, France"}]},{"given":"Maxime","family":"Chazalviel","sequence":"additional","affiliation":[{"name":"Medday Pharmaceuticals, Paris, France"}]},{"given":"Thomas","family":"Garcia","sequence":"additional","affiliation":[{"name":"Toxalim, Universit\u00e9 de Toulouse, INRA, Universit\u00e9 de Toulouse 3 Paul Sabatier, Toulouse, France"}]},{"given":"Florence","family":"Vinson","sequence":"additional","affiliation":[{"name":"Toxalim, Universit\u00e9 de Toulouse, INRA, Universit\u00e9 de Toulouse 3 Paul Sabatier, Toulouse, France"}]},{"given":"Nicolas","family":"Weiss","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de R\u00e9animation Neurologique, D\u00e9partement de Neurologie, P\u00f4le des Maladies du Syst\u00e8me Nerveux Central, Groupement Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re Charles Foix, Assistance Publique \u2013 H\u00f4pitaux de Paris, Paris, France"},{"name":"Brain Liver Piti\u00e9-Salp\u00eatri\u00e8re (BLIPS) Study Group, Groupement Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re-Charles Foix, Assistance Publique \u2013 H\u00f4pitaux de Paris & INSERM UMR_S 938, CDR Saint-Antoine Maladies M\u00e9taboliques, Biliaires et Fibro-inflammatoire du Foie & Institut de Cardiom\u00e9tabolisme et Nutrition, ICAN, Paris, France"}]},{"given":"Benoit","family":"Colsch","sequence":"additional","affiliation":[{"name":"Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Universit\u00e9 Paris-Saclay, MetaboHUB, Gif-sur-Yvette, France and"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Sedel","sequence":"additional","affiliation":[{"name":"Medday Pharmaceuticals, Paris, France"}]},{"given":"Dominique","family":"Thabut","sequence":"additional","affiliation":[{"name":"Brain Liver Piti\u00e9-Salp\u00eatri\u00e8re (BLIPS) Study Group, Groupement Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re-Charles Foix, Assistance Publique \u2013 H\u00f4pitaux de Paris & INSERM UMR_S 938, CDR Saint-Antoine Maladies M\u00e9taboliques, Biliaires et Fibro-inflammatoire du Foie & Institut de Cardiom\u00e9tabolisme et Nutrition, ICAN, Paris, France"},{"name":"Unit\u00e9 de Soins Intensifs d\u2019H\u00e9pato-gastroent\u00e9rologie, Groupement Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re-Charles Foix, Assistance Publique \u2013 H\u00f4pitaux de Paris et Universit\u00e9 Pierre et Marie Curie Paris 6, Paris, France"}]},{"given":"Christophe","family":"Junot","sequence":"additional","affiliation":[{"name":"Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Universit\u00e9 Paris-Saclay, MetaboHUB, Gif-sur-Yvette, France and"}]},{"given":"Fabien","family":"Jourdan","sequence":"additional","affiliation":[{"name":"Toxalim, Universit\u00e9 de Toulouse, INRA, Universit\u00e9 de Toulouse 3 Paul Sabatier, Toulouse, France"}]}],"member":"286","published-online":{"date-parts":[[2018,7,6]]},"reference":[{"key":"2023013107230121400_bty577-B1","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1016\/S0022-510X(99)00169-0","article-title":"Hepatic encephalopathy: molecular mechanisms underlying the clinical syndrome","volume":"170","author":"Albrecht","year":"1999","journal-title":"J. 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