{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T22:10:19Z","timestamp":1675203019701},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: ChIP\u2013chip has been widely used for various genome-wide biological investigations. Given the small number of replicates (typically two to three) per biological sample, methods of analysis that control the variance are desirable but in short supply. We propose a double error shrinkage (DES) method by using moving average statistics based on local-pooled error estimates which effectively control both heterogeneous error variances and correlation structures of an extremely large number of individual probes on tiling arrays.<\/jats:p>\n               <jats:p>Results: Applying DES to ChIP\u2013chip tiling array study for discovering genome-wide protein-binding sites, we identified 8400 target regions that include highly likely TFIID binding sites. About 33% of these were well matched with the known transcription starting sites on the DBTSS library, while many other newly identified sites have a high chance to be real binding sites based on a high positive predictive value of DES. We also showed the superior performance of DES compared with other commonly used methods for detecting actual protein binding sites.<\/jats:p>\n               <jats:p>Contact: \u00a0tspark@snu.ac.kr; jaeklee@virginia.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp471","type":"journal-article","created":{"date-parts":[[2009,8,11]],"date-time":"2009-08-11T01:06:19Z","timestamp":1249952779000},"page":"2486-2491","source":"Crossref","is-referenced-by-count":1,"title":["Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication"],"prefix":"10.1093","volume":"25","author":[{"given":"Youngchul","family":"Kim","sequence":"first","affiliation":[{"name":"1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA"},{"name":"1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA"}]},{"given":"Stefan","family":"Bekiranov","sequence":"additional","affiliation":[{"name":"1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA"}]},{"given":"Jae K.","family":"Lee","sequence":"additional","affiliation":[{"name":"1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA"}]},{"given":"Taesung","family":"Park","sequence":"additional","affiliation":[{"name":"1 Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA, 2Department of Statistics, Seoul National University, Seoul, Korea and 3Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,8,10]]},"reference":[{"key":"2023013112124806100_B1","doi-asserted-by":"crossref","first-page":"R97","DOI":"10.1186\/gb-2005-6-11-r97","article-title":"ChIPoTle: a user-friendly tool for the analysis of ChIP-chip data","volume":"6","author":"Buck","year":"2005","journal-title":"Genome Biol."},{"key":"2023013112124806100_B2","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/S0092-8674(04)00127-8","article-title":"Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs","volume":"116","author":"Cawley","year":"2004","journal-title":"Cell"},{"key":"2023013112124806100_B3","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nature02800","article-title":"Transcriptional regulatory code of a eukaryotic genome","volume":"431","author":"Harbison","year":"2004","journal-title":"Nature"},{"key":"2023013112124806100_B4","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nature07829","article-title":"Histone modifications at human enhancers reflect global cell-type-specific gene expression","volume":"459","author":"Heintzman","year":"2009","journal-title":"Nature"},{"key":"2023013112124806100_B5","doi-asserted-by":"crossref","first-page":"1945","DOI":"10.1093\/bioinformatics\/btg264","article-title":"Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays","volume":"19","author":"Jain","year":"2003","journal-title":"Bioinformatics"},{"key":"2023013112124806100_B6","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1101\/gr.7080508","article-title":"Systematic evaluation of variability in ChIP-chip experiments using predefined DNA target","volume":"18","author":"Johnson","year":"2008","journal-title":"Genome Res."},{"key":"2023013112124806100_B7","doi-asserted-by":"crossref","first-page":"12457","DOI":"10.1073\/pnas.0601180103","article-title":"Model-based analysis of tiling-arrays for ChIP-chip","volume":"103","author":"Johnson","year":"2006","journal-title":"Proc. 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