{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T04:05:24Z","timestamp":1783483524524,"version":"3.55.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: Gene copy number and DNA methylation alterations are key regulators of gene expression in cancer. Accordingly, genes that show simultaneous methylation, copy number and expression alterations are likely to have a key role in tumor progression. We have implemented a novel software package (CNAmet) for integrative analysis of high-throughput copy number, DNA methylation and gene expression data. To demonstrate the utility of CNAmet, we use copy number, DNA methylation and gene expression data from 50 glioblastoma multiforme and 188 ovarian cancer primary tumor samples. Our results reveal a synergistic effect of DNA methylation and copy number alterations on gene expression for several known oncogenes as well as novel candidate oncogenes.<\/jats:p><jats:p>Availability: CNAmet R-package and user guide are freely available under GNU General Public License at http:\/\/csbi.ltdk.helsinki.fi\/CNAmet.<\/jats:p><jats:p>Contact: \u00a0sampsa.hautaniemi@helsinki.fi<\/jats:p><jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr019","type":"journal-article","created":{"date-parts":[[2011,1,13]],"date-time":"2011-01-13T02:19:41Z","timestamp":1294885181000},"page":"887-888","source":"Crossref","is-referenced-by-count":103,"title":["CNAmet: an R package for integrating copy number, methylation and expression data"],"prefix":"10.1093","volume":"27","author":[{"given":"Riku","family":"Louhimo","sequence":"first","affiliation":[{"name":"Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sampsa","family":"Hautaniemi","sequence":"additional","affiliation":[{"name":"Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,1,12]]},"reference":[{"key":"2023012511553651500_B1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. 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