{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T05:39:01Z","timestamp":1740202741920,"version":"3.37.3"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Chromatin immunoprecipitation followed by genome tiling array hybridization (ChIP-chip) is a powerful approach to identify transcription factor binding sites (TFBSs) in target genomes. When multiple related ChIP-chip datasets are available, analyzing them jointly allows one to borrow information across datasets to improve peak detection. This is particularly useful for analyzing noisy datasets.<\/jats:p><jats:p>Results: We propose a hierarchical mixture model and develop an R package JAMIE to perform the joint analysis. The genome is assumed to consist of background and potential binding regions (PBRs). PBRs have context-dependent probabilities to become bona fide binding sites in individual datasets. This model captures the correlation among datasets, which provides basis for sharing information across experiments. Real data tests illustrate the advantage of JAMIE over a strategy that analyzes individual datasets separately.<\/jats:p><jats:p>Availability: \u00a0JAMIE is freely available from http:\/\/www.biostat.jhsph.edu\/\u223chji\/jamie<\/jats:p><jats:p>Contact: \u00a0hji@jhsph.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq314","type":"journal-article","created":{"date-parts":[[2010,6,16]],"date-time":"2010-06-16T01:09:58Z","timestamp":1276650598000},"page":"1864-1870","source":"Crossref","is-referenced-by-count":7,"title":["JAMIE: joint analysis of multiple ChIP-chip experiments"],"prefix":"10.1093","volume":"26","author":[{"given":"Hao","family":"Wu","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA"}]},{"given":"Hongkai","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,6,15]]},"reference":[{"key":"2023012507594940600_B1","doi-asserted-by":"crossref","first-page":"D5","DOI":"10.1093\/nar\/gkn764","article-title":"NCBI GEO: archive for high-throughput functional genomic data","volume":"37","author":"Barrett","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012507594940600_B2","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high density oligonucleotide array data based on variance and bias","volume":"19","author":"Bolstad","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012507594940600_B3","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1016\/j.cell.2005.08.020","article-title":"Core transcriptional regulatory circuitry in human embryonic stem cells","volume":"122","author":"Boyer","year":"2005","journal-title":"Cell"},{"key":"2023012507594940600_B4","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.cell.2005.05.008","article-title":"Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1","volume":"122","author":"Carroll","year":"2005","journal-title":"Cell"},{"key":"2023012507594940600_B5","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":"2023012507594940600_B6","doi-asserted-by":"crossref","first-page":"1715","DOI":"10.1093\/bioinformatics\/btp312","article-title":"Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data","volume":"25","author":"Choi","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012507594940600_B7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.2517-6161.1977.tb01600.x","article-title":"Maximum likelihood from incomplete data via the EM algorithm","volume":"39","author":"Dempster","year":"1977","journal-title":"J. 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