{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:19:29Z","timestamp":1772173169859,"version":"3.50.1"},"reference-count":75,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2023,3,9]],"date-time":"2023-03-09T00:00:00Z","timestamp":1678320000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006489","name":"Commissariat \u00e0 l\u2019\u00c9nergie Atomique et aux \u00c9nergies Alternatives","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006489","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012952","name":"Universit\u00e9 Grenoble Alpes","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012952","id-type":"DOI","asserted-by":"publisher"}]},{"name":"MINES ParisTech: Mines Paris - PSL"},{"DOI":"10.13039\/501100001677","name":"Institut national de la sant\u00e9 et de la recherche m\u00e9dicale","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001677","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>The majority of gene expression studies focus on the search for genes whose mean expression is different between two or more populations of samples in the so-called \u201cdifferential expression analysis\u201d approach. However, a difference in variance in gene expression may also be biologically and physiologically relevant. In the classical statistical model used to analyze RNA-sequencing (RNA-seq) data, the dispersion, which defines the variance, is only considered as a parameter to be estimated prior to identifying a difference in mean expression between conditions of interest. Here, we propose to evaluate four recently published methods, which detect differences in both the mean and dispersion in RNA-seq data. We thoroughly investigated the performance of these methods on simulated datasets and characterized parameter settings to reliably detect genes with a differential expression dispersion. We applied these methods to The Cancer Genome Atlas datasets. Interestingly, among the genes with an increased expression dispersion in tumors and without a change in mean expression, we identified some key cellular functions, most of which were related to catabolism and were overrepresented in most of the analyzed cancers. In particular, our results highlight autophagy, whose role in cancerogenesis is context-dependent, illustrating the potential of the differential dispersion approach to gain new insights into biological processes and to discover new biomarkers.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1010342","type":"journal-article","created":{"date-parts":[[2023,3,9]],"date-time":"2023-03-09T13:25:23Z","timestamp":1678368323000},"page":"e1010342","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Detection of genes with differential expression dispersion unravels the role of autophagy in cancer progression"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9411-0176","authenticated-orcid":true,"given":"Christophe","family":"Le Priol","sequence":"first","affiliation":[]},{"given":"Chlo\u00e9-Agathe","family":"Azencott","sequence":"additional","affiliation":[]},{"given":"Xavier","family":"Gidrol","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2023,3,9]]},"reference":[{"issue":"11","key":"pcbi.1010342.ref001","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1038\/nbt.2421","article-title":"The expanding scope of DNA sequencing","volume":"30","author":"J Shendure","year":"2012","journal-title":"Nat Biotechnol"},{"issue":"10A","key":"pcbi.1010342.ref002","doi-asserted-by":"crossref","first-page":"1938","DOI":"10.1101\/gr.2890204","article-title":"Quantification of multiple gene expression in individual cells","volume":"14","author":"A Peixoto","year":"2004","journal-title":"Genome Res"},{"issue":"3","key":"pcbi.1010342.ref003","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1101\/gr.3124505","article-title":"Database of mRNA gene expression 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