{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T12:19:52Z","timestamp":1775218792860,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: While meta-analysis provides a powerful tool for analyzing microarray experiments by combining data from multiple studies, it presents unique computational challenges. The Bioconductor package RankProd provides a new and intuitive tool for this purpose in detecting differentially expressed genes under two experimental conditions. The package modifies and extends the rank product method proposed by Breitling et al., [(2004)FEBS Lett., 573, 83\u201392] to integrate multiple microarray studies from different laboratories and\/or platforms. It offers several advantages over t-test based methods and accepts pre-processed expression datasets produced from a wide variety of platforms. The significance of the detection is assessed by a non-parametric permutation test, and the associated P-value and false discovery rate (FDR) are included in the output alongside the genes that are detected by user-defined criteria. A visualization plot is provided to view actual expression levels for each gene with estimated significance measurements.<\/jats:p>\n               <jats:p>Availability: RankProd is available at Bioconductor . A web-based interface will soon be available at<\/jats:p>\n               <jats:p>Contact: \u00a0fhong@salk.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl476","type":"journal-article","created":{"date-parts":[[2006,9,19]],"date-time":"2006-09-19T00:42:24Z","timestamp":1158626544000},"page":"2825-2827","source":"Crossref","is-referenced-by-count":609,"title":["RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis"],"prefix":"10.1093","volume":"22","author":[{"given":"Fangxin","family":"Hong","sequence":"first","affiliation":[{"name":"Plant Biology Laboratory 1 \u00a0 1 \u00a0 \u00a0 La Jolla, CA, USA"},{"name":"Howard Hughes Medical Institute, The Salk Institute 2 \u00a0 2 \u00a0 \u00a0 La Jolla, CA, USA"}]},{"given":"Rainer","family":"Breitling","sequence":"additional","affiliation":[{"name":"Groningen Bioinformatics Centre, University of Groningen 3 \u00a0 3 \u00a0 \u00a0 Haren, The Netherlands"}]},{"given":"Connor W.","family":"McEntee","sequence":"additional","affiliation":[{"name":"Plant Biology Laboratory 1 \u00a0 1 \u00a0 \u00a0 La Jolla, CA, USA"}]},{"given":"Ben S.","family":"Wittner","sequence":"additional","affiliation":[{"name":"Center for Cancer Research, Massachusetts General Hospital 4 \u00a0 4 \u00a0 \u00a0 Boston, MA, USA"}]},{"given":"Jennifer L.","family":"Nemhauser","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Washington 5 \u00a0 5 \u00a0 \u00a0 Seattle, WA, USA"}]},{"given":"Joanne","family":"Chory","sequence":"additional","affiliation":[{"name":"Plant Biology Laboratory 1 \u00a0 1 \u00a0 \u00a0 La Jolla, CA, USA"},{"name":"Howard Hughes Medical Institute, The Salk Institute 2 \u00a0 2 \u00a0 \u00a0 La Jolla, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2006,9,18]]},"reference":[{"key":"2023012408425451800_b1","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.febslet.2004.07.055","article-title":"Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments","volume":"573","author":"Breitling","year":"2004","journal-title":"FEBS Lett."},{"key":"2023012408425451800_b2","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1142\/S0219720005001442","article-title":"Rank-based methods as a non-parametric alternative of the T-statistic for the analysis of biological microarray data","volume":"3","author":"Breitling","year":"2005","journal-title":"J. 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