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To facilitate phenotype-oriented gene set analysis, we developed PhenoExam, a freely available R package for tool developers and a web interface for users, which performs: (1) phenotype and disease enrichment analysis on a gene set; (2) measures statistically significant phenotype similarities between gene sets and (3) detects significant differential phenotypes or disease terms across different databases.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>PhenoExam generates sensitive and accurate phenotype enrichment analyses. It is also effective in segregating gene sets or Mendelian diseases with very similar phenotypes. We tested the tool with two similar diseases (Parkinson and dystonia), to show phenotype-level similarities but also potentially interesting differences. Moreover, we used PhenoExam to validate computationally predicted new genes potentially associated with epilepsy.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>We developed PhenoExam, a freely available R package and Web application, which performs phenotype enrichment and disease enrichment analysis on gene set G, measures statistically significant phenotype similarities between pairs of gene sets G and G\u2032 and detects statistically significant exclusive phenotypes or disease terms, across different databases. We proved with simulations and real cases that it is useful to distinguish between gene sets or diseases with very similar phenotypes.<\/jats:p>\n                <jats:p>Github R package URL is <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/alexcis95\/PhenoExam\">https:\/\/github.com\/alexcis95\/PhenoExam<\/jats:ext-link>.<\/jats:p>\n                <jats:p>Shiny App URL is <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/alejandrocisterna.shinyapps.io\/phenoexamweb\/\">https:\/\/alejandrocisterna.shinyapps.io\/phenoexamweb\/<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-022-05122-x","type":"journal-article","created":{"date-parts":[[2022,12,31]],"date-time":"2022-12-31T16:03:03Z","timestamp":1672502583000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["PhenoExam: gene set analyses through integration of different phenotype databases"],"prefix":"10.1186","volume":"23","author":[{"given":"Alejandro","family":"Cisterna","sequence":"first","affiliation":[]},{"given":"Aurora","family":"Gonz\u00e1lez-Vidal","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"Ruiz","sequence":"additional","affiliation":[]},{"given":"Jordi","family":"Ortiz","sequence":"additional","affiliation":[]},{"given":"Alicia","family":"G\u00f3mez-Pascual","sequence":"additional","affiliation":[]},{"given":"Zhongbo","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Mike","family":"Nalls","sequence":"additional","affiliation":[]},{"given":"Faraz","family":"Faghri","sequence":"additional","affiliation":[]},{"given":"John","family":"Hardy","sequence":"additional","affiliation":[]},{"given":"Irene","family":"D\u00edez","sequence":"additional","affiliation":[]},{"given":"Paolo","family":"Maietta","sequence":"additional","affiliation":[]},{"given":"Sara","family":"\u00c1lvarez","sequence":"additional","affiliation":[]},{"given":"Mina","family":"Ryten","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6992-598X","authenticated-orcid":false,"given":"Juan A.","family":"Bot\u00eda","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,12,31]]},"reference":[{"issue":"6822","key":"5122_CR1","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1038\/35057050","volume":"409","author":"G Jimenez-Sanchez","year":"2001","unstructured":"Jimenez-Sanchez G, Childs B, Valle D. 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