{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T22:50:59Z","timestamp":1767826259641,"version":"3.49.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Over the past years growing knowledge about biological processes and pathways revealed complex interaction networks involving many genes. In order to understand these networks, analysis of differential expression has continuously moved from single genes towards the study of gene sets. Various approaches for the assessment of gene sets have been developed in the context of gene set analysis (GSA). These approaches are bridging the gap between raw measurements and semantically meaningful terms.<\/jats:p>\n               <jats:p>We present a novel approach for assessing uncertainty in the definition of gene sets. This is an essential step when new gene sets are constructed from domain knowledge or given gene sets are suspected to be affected by uncertainty. Quantification of uncertainty is implemented in the R-package GiANT. We also included widely used GSA methods, embedded in a generic framework that can readily be extended by custom methods. The package provides an easy to use front end and allows for fast parallelization.<\/jats:p>\n               <jats:p>Availability and implementation: The package GiANT is available on CRAN.<\/jats:p>\n               <jats:p>Contacts: \u00a0hans.kestler@leibniz-fli.de or hans.kestler@uni-ulm.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw030","type":"journal-article","created":{"date-parts":[[2016,2,15]],"date-time":"2016-02-15T01:09:07Z","timestamp":1455498547000},"page":"1891-1894","source":"Crossref","is-referenced-by-count":9,"title":["GiANT: gene set uncertainty in enrichment analysis"],"prefix":"10.1093","volume":"32","author":[{"given":"Florian","family":"Schmid","sequence":"first","affiliation":[{"name":"1 Institute of Medical Systems Biology, Ulm University, Ulm 89069, Germany,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthias","family":"Schmid","sequence":"additional","affiliation":[{"name":"2 Institut f\u00fcr Medizinische Biometrie, Informatik und Epidemiologie, Universit\u00e4t Bonn, Bonn 53127, Germany,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christoph","family":"M\u00fcssel","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Systems Biology, Ulm University, Ulm 89069, Germany,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J. Eric","family":"Str\u00e4ng","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Systems Biology, Ulm University, Ulm 89069, Germany,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Buske","sequence":"additional","affiliation":[{"name":"3 Institute of Experimental Cancer Research,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lars","family":"Bullinger","sequence":"additional","affiliation":[{"name":"4 Department of Internal Medicine III, Ulm University, Ulm 89069, Germany and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johann M.","family":"Kraus","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Systems Biology, Ulm University, Ulm 89069, Germany,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hans A.","family":"Kestler","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Systems Biology, Ulm University, Ulm 89069, Germany,"},{"name":"5 Leibniz Institute on Ageing \u2013 Fritz Lipmann Institute and FSU Jena, Jena 07745, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,2,1]]},"reference":[{"key":"2023020112320247600_btw030-B1","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/1471-2105-10-47","article-title":"A general modular framework for gene set enrichment analysis","volume":"10","author":"Ackermann","year":"2009","journal-title":"BMC Bioinf"},{"key":"2023020112320247600_btw030-B2","doi-asserted-by":"crossref","first-page":"1592","DOI":"10.1093\/bioinformatics\/btv023","article-title":"Bias in microRNA functional enrichment analysis","volume":"31","author":"Bleazard","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020112320247600_btw030-B3","doi-asserted-by":"crossref","first-page":"W329","DOI":"10.1093\/nar\/gkp263","article-title":"WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis","volume":"37","author":"Glez-Pe\u00f1a","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023020112320247600_btw030-B4","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1093\/bioinformatics\/btm051","article-title":"Analyzing gene expression data in terms of gene sets: methodological issues","volume":"23","author":"Goeman","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020112320247600_btw030-B5","doi-asserted-by":"crossref","first-page":"W169","DOI":"10.1093\/nar\/gkm415","article-title":"DAVID bioinformatics resources: expanded annotation database and novel algorithms to better extract biology from large gene lists","volume":"35","author":"Huang","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023020112320247600_btw030-B6","doi-asserted-by":"crossref","first-page":"D892","DOI":"10.1093\/nar\/gkt1073","article-title":"AgeFactDB \u2013 the JenAge Ageing Factor Database \u2013 towards data integration in ageing research","volume":"42","author":"H\u00fchne","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020112320247600_btw030-B7","doi-asserted-by":"crossref","first-page":"D428","DOI":"10.1093\/nar\/gki072","article-title":"Reactome: a knowledgebase of biological pathways","volume":"33","author":"Joshi-Tope","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023020112320247600_btw030-B8","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023020112320247600_btw030-B9","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1053\/j.gastro.2012.02.009","article-title":"Disruption of trp53 in livers of mice induces formation of carcinomas with bilineal differentiation","volume":"142","author":"Katz","year":"2012","journal-title":"Gastroenterology"},{"key":"2023020112320247600_btw030-B10","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1287\/opre.50.6.1073.358","article-title":"An object-oriented random-number package with many long streams and substreams","volume":"50","author":"L\u2019Ecuyer","year":"2002","journal-title":"Oper. 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