{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T14:51:54Z","timestamp":1761058314299},"reference-count":14,"publisher":"Springer Science and Business Media LLC","issue":"S2","license":[{"start":{"date-parts":[[2005,7,1]],"date-time":"2005-07-01T00:00:00Z","timestamp":1120176000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2005,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Gender differences in gene expression were estimated in liver samples from 9 males and 9 females. The study tested 31,110 genes for a gender difference using a design that adjusted for sources of variation associated with cDNA arrays, normalization, hybridizations and processing conditions.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The genes were split into 2,800 that were clearly expressed (expressed genes) and 28,310 that had expression levels in the background range (not expressed genes). The distribution of p-values from the 'not expressed' group was consistent with no gender differences. The distribution of p-values from the 'expressed' group suggested that 8 % of these genes differed by gender, but the estimated fold-changes (expression in males \/ expression in females) were small. The largest observed fold-change was 1.55. The 95 % confidence bounds on the estimated fold-changes were less than 1.4 fold for 79.3 %, and few (1.1%) exceed 2-fold.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Observed gender differences in gene expression were small. When selecting genes with gender differences based upon their p-values, false discovery rates exceed 80 % for any set of genes, essentially making it impossible to identify any specific genes with a gender difference.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-6-s2-s13","type":"journal-article","created":{"date-parts":[[2005,7,16]],"date-time":"2005-07-16T09:00:41Z","timestamp":1121504441000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Genome-wide estimation of gender differences in the gene expression of human livers: Statistical design and analysis"],"prefix":"10.1186","volume":"6","author":[{"given":"Robert R","family":"Delongchamp","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cruz","family":"Velasco","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stacey","family":"Dial","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Angela J","family":"Harris","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,7,15]]},"reference":[{"key":"671_CR1","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1289\/ehp.98106511","volume":"2","author":"A Guillouzo","year":"1998","unstructured":"Guillouzo A: Liver cell models in in vitro toxicology. Environmental Health Perspectives 1998, 2: 511\u2013532.","journal-title":"Environmental Health Perspectives"},{"key":"671_CR2","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1016\/S0041-1345(00)01154-4","volume":"32","author":"N Kobayashi","year":"2000","unstructured":"Kobayashi N, Noguchi H, Fujiwara T, Tanaka N: Establishment of a reversibly immortalized human hepatocyte cell line by using cre\/loxp site-specific recombination. Transplantation Proceedings 2000, 32: 1121\u20131122. 10.1016\/S0041-1345(00)01154-4","journal-title":"Transplantation Proceedings"},{"key":"671_CR3","doi-asserted-by":"publisher","first-page":"8971","DOI":"10.1073\/pnas.93.17.8971","volume":"93","author":"KA Westerman","year":"1996","unstructured":"Westerman KA, Leboulch P: Reversible immortalization of mammalian cells mediated by retroviral transfer and site-specific recombination. Proceedings of the National Academy of Sciences of the United States of America 1996, 93: 8971\u20138976. 10.1073\/pnas.93.17.8971","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"671_CR4","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1038\/nrg863","volume":"3","author":"YH Yang","year":"2002","unstructured":"Yang YH, Speed T: Design issues for cDNA microarray experiments. Nature Reviews Genetics 2002, 3: 579\u2013588.","journal-title":"Nature Reviews Genetics"},{"key":"671_CR5","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1016\/j.mrfmmm.2003.11.016","volume":"549","author":"VG Desai","year":"2004","unstructured":"Desai VG, Moland CL, Branham WS, Delongchamp RR, Fang H, Duffy PH, Peterson CA, Beggs ML, Fuscoe JC: Changes in expression level of genes as a function of time of day in the liver of rats. Mutation Research \u2013 Fundamental & Molecular Mechanisms of Mutagenesis 2004, 549: 115\u2013129. 10.1016\/j.mrfmmm.2003.11.016","journal-title":"Mutation Research \u2013 Fundamental & Molecular Mechanisms of Mutagenesis"},{"key":"671_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0167-9473(01)00046-9","volume":"39","author":"DB Allison","year":"2002","unstructured":"Allison DB, Gadbury GL, Heo M, Fernandez JR, Lee C-K, Prolla TA, Weindruch R: A mixture model approach for the analysis of microarray gene expression data. Computational Statistics and Data Analysis 2002, 39: 1\u201320. 10.1016\/S0167-9473(01)00046-9","journal-title":"Computational Statistics and Data Analysis"},{"key":"671_CR7","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1111\/j.0006-341X.2004.00228.x","volume":"60","author":"RR Delongchamp","year":"2004","unstructured":"Delongchamp RR, Bowyer JF, Chen J, Kodell RL: Multiple-testing strategy for analyzing cDNA array data on gene expression. Biometrics 2004, 60: 774\u2013782. 10.1111\/j.0006-341X.2004.00228.x","journal-title":"Biometrics"},{"key":"671_CR8","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1089\/106652702760277372","volume":"9","author":"KR Coombes","year":"2002","unstructured":"Coombes KR, Highsmith WE, Krogmann TA, Baggerly KA, Stivers DN, Abruzzo LV: Identifying and quantifying sources of variation in microarray data using high-density cDNA membrane arrays. Journal of Computational Biology 2002, 9: 655\u2013670. 10.1089\/106652702760277372","journal-title":"Journal of Computational Biology"},{"key":"671_CR9","volume-title":"DNA microarrays and statistical genomic techniques: Design, analysis, and interpretation of experiments","author":"RS Parrish","year":"2005","unstructured":"Parrish RS, Delongchamp RR: Normalization. In DNA microarrays and statistical genomic techniques: Design, analysis, and interpretation of experiments. Edited by: Allison DB, Page GP, Beasley TM, Edwards JW. New York: Marcel Dekker, Inc; 2005:in press."},{"key":"671_CR10","unstructured":"Sas\/stat users guide, version 8. Cary, NC: SAS Institute Inc; 1999."},{"key":"671_CR11","doi-asserted-by":"publisher","first-page":"9834","DOI":"10.1073\/pnas.97.18.9834","volume":"97","author":"MLT Lee","year":"2000","unstructured":"Lee MLT, Kuo FC, Whitmore GA, Sklar J: Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations. Proceedings of the National Academy of Sciences of the United States of America 2000, 97: 9834\u20139839. 10.1073\/pnas.97.18.9834","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"671_CR12","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1093\/biomet\/69.3.493","volume":"69","author":"T Schweder","year":"1982","unstructured":"Schweder T, Spjotvoll E: Plots of p-values to evaluate many tests simultaneously. Biometrika 1982, 69: 493\u2013502. 10.2307\/2335984","journal-title":"Biometrika"},{"key":"671_CR13","doi-asserted-by":"publisher","first-page":"1073","DOI":"10.1111\/j.0006-341X.2003.00123.x","volume":"59","author":"C-A Tsai","year":"2003","unstructured":"Tsai C-A, Hsueh H-m, Chen JJ: Estimation of false discovery rates in multiple testing: Application to gene microarray data. Biometrics 2003, 59: 1073\u20131083. 10.1111\/j.0006-341X.2003.00123.x","journal-title":"Biometrics"},{"key":"671_CR14","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1081\/BIP-120024202","volume":"13","author":"H-m Hsueh","year":"2003","unstructured":"Hsueh H-m, Chen JJ, Kodell RL: Comparison of methods for estimating the number of true hypotheses in multiplicity testing. Journal of Biopharmaceutical Statistics 2003, 13: 675\u2013689. 10.1081\/BIP-120024202","journal-title":"Journal of Biopharmaceutical Statistics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-S2-S13.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-6-S2-S13\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-S2-S13.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T21:19:52Z","timestamp":1630444792000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-S2-S13"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,7]]},"references-count":14,"journal-issue":{"issue":"S2","published-print":{"date-parts":[[2005,7]]}},"alternative-id":["671"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-s2-s13","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,7]]},"assertion":[{"value":"15 July 2005","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S13"}}