{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T20:32:02Z","timestamp":1774470722173,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,11,10]],"date-time":"2016-11-10T00:00:00Z","timestamp":1478736000000},"content-version":"vor","delay-in-days":73,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["U24CA143835"],"award-info":[{"award-number":["U24CA143835"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Combining P-values from multiple statistical tests is a common exercise in bioinformatics. However, this procedure is non-trivial for dependent P-values. Here, we discuss an empirical adaptation of Brown\u2019s method (an extension of Fisher\u2019s method) for combining dependent P-values which is appropriate for the large and correlated datasets found in high-throughput biology.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We show that the Empirical Brown\u2019s method (EBM) outperforms Fisher\u2019s method as well as alternative approaches for combining dependent P-values using both noisy simulated data and gene expression data from The Cancer Genome Atlas.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>The Empirical Brown\u2019s method is available in Python, R, and MATLAB and can be obtained from https:\/\/github.com\/IlyaLab\/CombiningDependentPvalues UsingEBM. The R code is also available as a Bioconductor package from https:\/\/www.bioconductor.org\/packages\/devel\/bioc\/html\/EmpiricalBrownsMethod.html.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Contact<\/jats:title>\n                    <jats:p>Theo.Knijnenburg@systemsbiology.org<\/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\/btw438","type":"journal-article","created":{"date-parts":[[2016,9,1]],"date-time":"2016-09-01T03:53:39Z","timestamp":1472702019000},"page":"i430-i436","source":"Crossref","is-referenced-by-count":138,"title":["Combining dependent\n                    <i>P-<\/i>\n                    values with an empirical adaptation of Brown\u2019s method"],"prefix":"10.1093","volume":"32","author":[{"given":"William","family":"Poole","sequence":"first","affiliation":[{"name":"Institute for Systems Biology, Seattle, WA 98109-5263, USA"}]},{"given":"David L","family":"Gibbs","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology, Seattle, WA 98109-5263, USA"}]},{"given":"Ilya","family":"Shmulevich","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology, Seattle, WA 98109-5263, USA"}]},{"given":"Brady","family":"Bernard","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology, Seattle, WA 98109-5263, USA"}]},{"given":"Theo A","family":"Knijnenburg","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology, Seattle, WA 98109-5263, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,8,29]]},"reference":[{"key":"2023020113280240500_btw438-B1","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/nbt1203","article-title":"Gene prioritization through genomic data fusion","volume":"24","author":"Aerts","year":"2006","journal-title":"Nat. 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