{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T19:26:47Z","timestamp":1773862007696,"version":"3.50.1"},"reference-count":13,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,2,17]],"date-time":"2020-02-17T00:00:00Z","timestamp":1581897600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,2,17]],"date-time":"2020-02-17T00:00:00Z","timestamp":1581897600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Fonds Wetenschappelijk Onderzoek","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Vocatio"},{"DOI":"10.13039\/501100011851","name":"Kom op tegen Kanker","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100011851","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100005026","name":"Stichting Tegen Kanker","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100005026","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>To understand biology and differences among various tissues or cell types, one typically searches for molecular features that display characteristic abundance patterns. Several specificity metrics have been introduced to identify tissue-specific molecular features, but these either require an equal number of replicates per tissue or they can\u2019t handle replicates at all.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We describe a non-parametric specificity score that is compatible with unequal sample group sizes. To demonstrate its usefulness, the specificity score was calculated on all GTEx samples, detecting known and novel tissue-specific genes. A webtool was developed to browse these results for genes or tissues of interest. An example python implementation of SPECS is available at\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/celineeveraert\/SPECS\">https:\/\/github.com\/celineeveraert\/SPECS<\/jats:ext-link>\n                      . The precalculated SPECS results on the GTEx data are available through a user-friendly browser at\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/specs.cmgg.be\">specs.cmgg.be<\/jats:ext-link>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>SPECS is a non-parametric method that identifies known and novel specific-expressed genes. In addition, SPECS could be adopted for other features and applications.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-020-3407-z","type":"journal-article","created":{"date-parts":[[2020,2,17]],"date-time":"2020-02-17T09:07:45Z","timestamp":1581930465000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["SPECS: a non-parametric method to identify tissue-specific molecular features for unbalanced sample groups"],"prefix":"10.1186","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7772-4259","authenticated-orcid":false,"given":"Celine","family":"Everaert","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pieter-Jan","family":"Volders","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Annelien","family":"Morlion","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Thas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pieter","family":"Mestdagh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,2,17]]},"reference":[{"key":"3407_CR1","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1038\/nature17161","volume":"531","author":"E Leucci","year":"2016","unstructured":"Leucci E, Vendramin R, Spinazzi M, Laurette P, Fiers M, Wouters J, et al. Melanoma addiction to the long non-coding RNA SAMMSON. Nature. 2016;531:518\u201322. https:\/\/doi.org\/10.1038\/nature17161.","journal-title":"Nature"},{"key":"3407_CR2","doi-asserted-by":"publisher","first-page":"5443","DOI":"10.1200\/JCO.2007.13.6531","volume":"26","author":"J Stutterheim","year":"2008","unstructured":"Stutterheim J, Gerritsen A, Zappeij-Kannegieter L, Kleijn I, Dee R, Hooft L, et al. PHOX2B is a novel and specific marker for minimal residual disease testing in neuroblastoma. J Clin Oncol. 2008;26:5443\u20139. https:\/\/doi.org\/10.1200\/JCO.2007.13.6531.","journal-title":"J Clin Oncol"},{"key":"3407_CR3","doi-asserted-by":"publisher","first-page":"1392","DOI":"10.1038\/ng.2771","volume":"45","author":"JR Prensner","year":"2013","unstructured":"Prensner JR, Iyer MK, Sahu A, Asangani IA, Cao Q, Patel L, et al. The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI\/SNF complex. Nat Genet. 2013;45:1392\u20138. https:\/\/doi.org\/10.1038\/ng.2771.","journal-title":"Nat Genet"},{"key":"3407_CR4","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1038\/ng.2653","volume":"45","author":"J Lonsdale","year":"2013","unstructured":"Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, et al. The genotype-tissue expression (GTEx) project. Nat Genet. 2013;45:580\u20135. https:\/\/doi.org\/10.1038\/ng.2653.","journal-title":"Nat Genet"},{"key":"3407_CR5","doi-asserted-by":"publisher","first-page":"650","DOI":"10.1093\/bioinformatics\/bti042","volume":"21","author":"I Yanai","year":"2005","unstructured":"Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics. 2005;21:650\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/bti042.","journal-title":"Bioinformatics"},{"key":"3407_CR6","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1093\/nar\/gkp866","volume":"38","author":"A Vandenbon","year":"2009","unstructured":"Vandenbon A, Nakai K. Modeling tissue-specific structural patterns in human and mouse promoters. Nucleic Acids Res. 2009;38:17\u201325.","journal-title":"Nucleic Acids Res"},{"key":"3407_CR7","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1007\/s10888-011-9188-x","volume":"10","author":"L Ceriani","year":"2012","unstructured":"Ceriani L, Verme P. The origins of the Gini index: extracts from Variabilit\u00e0 e Mutabilit\u00e0 (1912) by Corrado Gini. J Econ Inequal. 2012;10:421\u201343.","journal-title":"J Econ Inequal"},{"key":"3407_CR8","doi-asserted-by":"publisher","first-page":"e1001328","DOI":"10.1371\/journal.pbio.1001328","volume":"10","author":"P Julien","year":"2012","unstructured":"Julien P, Brawand D, Soumillon M, Necsulea A, Liechti A, Sch\u00fctz F, et al. Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol. 2012;10:e1001328. https:\/\/doi.org\/10.1371\/journal.pbio.1001328.","journal-title":"PLoS Biol"},{"key":"3407_CR9","doi-asserted-by":"publisher","first-page":"1915","DOI":"10.1101\/gad.17446611","volume":"25","author":"MN Cabili","year":"2011","unstructured":"Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25:1915\u201327.","journal-title":"Genes Dev"},{"key":"3407_CR10","doi-asserted-by":"publisher","first-page":"bbw008","DOI":"10.1093\/bib\/bbw008","volume":"18","author":"N Kryuchkova-Mostacci","year":"2016","unstructured":"Kryuchkova-Mostacci N, Robinson-Rechavi M. A benchmark of gene expression tissue-specificity metrics. Brief Bioinform. 2016;18:bbw008. https:\/\/doi.org\/10.1093\/bib\/bbw008.","journal-title":"Brief Bioinform"},{"key":"3407_CR11","doi-asserted-by":"publisher","first-page":"1602","DOI":"10.1198\/jasa.2011.tm11181","volume":"106","author":"B Efron","year":"2011","unstructured":"Efron B. Tweedie\u2019s formula and selection bias. J Am Stat Assoc. 2011;106:1602\u201314. https:\/\/doi.org\/10.1198\/jasa.2011.tm11181.","journal-title":"J Am Stat Assoc"},{"key":"3407_CR12","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1101\/gr.109173.110","volume":"21","author":"L Thorrez","year":"2010","unstructured":"Thorrez L, Bonner-Weir S, Van Mechelen I, Van Lommel L, Laudadio I, Aguayo-Mazzucato C, et al. Tissue-specific disallowance of housekeeping genes: the other face of cell differentiation. Genome Res. 2010;21:95\u2013105.","journal-title":"Genome Res"},{"key":"3407_CR13","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. https:\/\/doi.org\/10.1186\/s13059-014-0550-8.","journal-title":"Genome Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-020-3407-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-020-3407-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-020-3407-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,2,17]],"date-time":"2021-02-17T11:16:07Z","timestamp":1613560567000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-020-3407-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,2,17]]},"references-count":13,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["3407"],"URL":"https:\/\/doi.org\/10.1186\/s12859-020-3407-z","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/656397","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,2,17]]},"assertion":[{"value":"18 July 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 February 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 February 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"58"}}