{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T06:39:34Z","timestamp":1775111974066,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2017,7,3]],"date-time":"2017-07-03T00:00:00Z","timestamp":1499040000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["521-2012-2037"],"award-info":[{"award-number":["521-2012-2037"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002794","name":"Swedish Cancer Society","doi-asserted-by":"publisher","award":["150768"],"award-info":[{"award-number":["150768"]}],"id":[{"id":"10.13039\/501100002794","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007232","name":"Cancer Research Foundations of Radiumhemmet","doi-asserted-by":"publisher","award":["144063"],"award-info":[{"award-number":["144063"]}],"id":[{"id":"10.13039\/501100007232","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006313","name":"Swedish Childhood Cancer Foundation","doi-asserted-by":"publisher","award":["PR2015-0009"],"award-info":[{"award-number":["PR2015-0009"]}],"id":[{"id":"10.13039\/501100006313","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Multi-dimensional data generated via high-throughput experiments is increasingly used in conjunction with dimensionality reduction methods to ascertain if resulting separations of the data correspond with known classes. This is particularly useful to determine if a subset of the variables, e.g. genes in a specific pathway, alone can separate samples into these established classes. Despite this, the evaluation of class separations is often subjective and performed via visualization. Here we present the ClusterSignificance package; a set of tools designed to assess the statistical significance of class separations downstream of dimensionality reduction algorithms. In addition, we demonstrate the design and utility of the ClusterSignificance package and utilize it to determine the importance of long non-coding RNA expression in the identity of multiple hematological malignancies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ClusterSignificance is an R package available via Bioconductor (https:\/\/bioconductor.org\/packages\/ClusterSignificance) under GPL-3.<\/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\/btx393","type":"journal-article","created":{"date-parts":[[2017,6,26]],"date-time":"2017-06-26T11:08:47Z","timestamp":1498475327000},"page":"3126-3128","source":"Crossref","is-referenced-by-count":14,"title":["ClusterSignificance: a bioconductor package facilitating statistical analysis of class cluster separations in dimensionality reduced data"],"prefix":"10.1093","volume":"33","author":[{"given":"Jason T","family":"Serviss","sequence":"first","affiliation":[{"name":"Department of Oncology and Pathology, Karolinska University Hospital Solna, Cancer Center Karolinska, Stockholm, Sweden"}]},{"given":"Jesper R","family":"G\u00e5din","sequence":"additional","affiliation":[{"name":"Department of Medicine, Cardiovascular Medicine Unit, Karolinska University Hospital Solna, Center for Molecular Medicine, Stockholm, Sweden"}]},{"given":"Per","family":"Eriksson","sequence":"additional","affiliation":[{"name":"Department of Medicine, Cardiovascular Medicine Unit, Karolinska University Hospital Solna, Center for Molecular Medicine, Stockholm, Sweden"}]},{"given":"Lasse","family":"Folkersen","sequence":"additional","affiliation":[{"name":"Department of Medicine, Cardiovascular Medicine Unit, Karolinska University Hospital Solna, Center for Molecular Medicine, Stockholm, Sweden"},{"name":"Department of Bioinformatics, Technical University of Denmark, Copenhagen, Denmark"}]},{"given":"Dan","family":"Grand\u00e9r","sequence":"additional","affiliation":[{"name":"Department of Oncology and Pathology, Karolinska University Hospital Solna, Cancer Center Karolinska, Stockholm, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2017,7,3]]},"reference":[{"key":"2023020206472309200_btx393-B1","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1198\/016214508000000832","article-title":"A case study in pharmacologic colon imaging using principal curves in single photon emission computed tomography","volume":"103","author":"Caffo","year":"2008","journal-title":"J. Am. Stat. Assoc"},{"key":"2023020206472309200_btx393-B2","first-page":"27219.","article-title":"Laplacian eigenmaps and principal curves for high resolution pseudotemporal ordering of single-cell RNA-seq profiles","author":"Campbell","year":"2015","journal-title":"bioRxiv"},{"key":"2023020206472309200_btx393-B3","doi-asserted-by":"crossref","first-page":"243","DOI":"10.22237\/jmasm\/1036110240","article-title":"Extensions of the concept of exchangeability and their applications","volume":"1","author":"Good","year":"2002","journal-title":"J. Mod. Appl. Stat. Methods"},{"key":"2023020206472309200_btx393-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ins.2014.02.068","article-title":"A methodology to compare dimensionality reduction algorithms in terms of loss of quality","volume":"270","author":"Gracia","year":"2014","journal-title":"J. Inf. 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Surg"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/19\/3126\/49041573\/bioinformatics_33_19_3126.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/19\/3126\/49041573\/bioinformatics_33_19_3126.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:47:55Z","timestamp":1675320475000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/19\/3126\/3920605"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,7,3]]},"references-count":10,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2017,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx393","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,10,1]]},"published":{"date-parts":[[2017,7,3]]}}}