{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:08Z","timestamp":1740185108918,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,14]],"date-time":"2016-10-14T00:00:00Z","timestamp":1476403200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100005010","name":"Italian Association for Cancer Research","doi-asserted-by":"crossref","award":["IG17185"],"award-info":[{"award-number":["IG17185"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Italian Ministry of Education, University and Research"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>In the omic era, one of the main aims is to discover groups of functionally related genes that drive the difference between different conditions. To this end, a plethora of potentially useful multivariate statistical approaches has been proposed, but their evaluation is hindered by the absence of a gold standard. Here, we propose a method for simulating biological data \u2013 gene expression, RPKM\/FPKM or protein abundances \u2013 from two conditions, namely, a reference condition and a perturbation of it. Our approach is built upon probabilistic graphical models and is thus especially suited for testing topological approaches.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The simPATHy is an R package, it is open source and freely available on CRAN.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw642","type":"journal-article","created":{"date-parts":[[2016,10,11]],"date-time":"2016-10-11T14:19:40Z","timestamp":1476195580000},"page":"456-457","source":"Crossref","is-referenced-by-count":4,"title":["simPATHy: a new method for simulating data from perturbed biological PATHways"],"prefix":"10.1093","volume":"33","author":[{"given":"Elisa","family":"Salviato","sequence":"first","affiliation":[{"name":"Department of Biology, University of Padova, Padova, Italy"}]},{"given":"Vera","family":"Djordjilovi\u0107","sequence":"additional","affiliation":[{"name":"Department of Statistical Sciences, University of Padova, Padova, Italy"}]},{"given":"Monica","family":"Chiogna","sequence":"additional","affiliation":[{"name":"Department of Statistical Sciences, University of Padova, Padova, Italy"}]},{"given":"Chiara","family":"Romualdi","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Padova, Padova, Italy"}]}],"member":"286","published-online":{"date-parts":[[2016,10,14]]},"reference":[{"key":"2023020204403356500_btw642-B1","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1089\/106652700750050961","article-title":"Using Bayesian networks to analyze expression data","volume":"7","author":"Friedman","year":"2000","journal-title":"J. Comput. Biol"},{"key":"2023020204403356500_btw642-B2","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1214\/11-AOAS528","article-title":"More power via graph-structured tests for differential expression of gene networks","volume":"6","author":"Jacob","year":"2012","journal-title":"Ann. Appl. 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Physiol"},{"key":"2023020204403356500_btw642-B7","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1093\/bioinformatics\/btn577","article-title":"A novel signaling pathway impact analysis","volume":"25","author":"Tarca","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020204403356500_btw642-B8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0079217","article-title":"A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity","volume":"8","author":"Tarca","year":"2013","journal-title":"PLoS ONE"},{"key":"2023020204403356500_btw642-B9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-7-43","article-title":"Syntren: a generator of synthetic gene expression data for design and analysis of structure learning algorithms","volume":"7","author":"Van den Bulcke","year":"2006","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/3\/456\/49037378\/bioinformatics_33_3_456.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/3\/456\/49037378\/bioinformatics_33_3_456.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:41:30Z","timestamp":1675312890000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/3\/456\/2585047"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2016,10,14]]},"references-count":9,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2017,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw642","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2017,2,1]]},"published":{"date-parts":[[2016,10,14]]}}}