{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T09:10:11Z","timestamp":1687857011224},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Chromatin immunoprecipitation (ChIP) is a powerful experimental approach to identify in vivo binding sites of sequence-specific transcription factors (TFs). These experiments are designed to specifically enrich DNA fragments that are bound to the TF. Tiling arrays have become more and more popular for the identification of these DNA fragments. However, many studies showed that only a fraction of the identified DNA fragments contains bona fide binding sites for the TF, suggesting that indirect binding mechanisms play a very important role. We explored the possibility that the lack of binding sites can also be explained by problems in identifying ChIP-enriched DNA fragments from the measured intensities.<\/jats:p>\n               <jats:p>Results: We derived a physical model that explains some (but not all) variation of the measured probe intensities of Affymetrix tilling arrays. We used the physical model to estimate the probe-specific behavior and corrected for it. Subsequently, we developed a method to identify ChIP-enriched DNA fragments. We termed it physical model for tiling array analysis (PMT). We applied PMT to the data of ChIP-chip experiments interrogating chromosome 21 and 22 of the human genome for binding of the TFs MYC, SP1 and P53. Almost all regions recovered by PMT showed evidence for sequence-specific binding of the TFs.<\/jats:p>\n               <jats:p>Contact: chung@molgen.mpg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm167","type":"journal-article","created":{"date-parts":[[2007,7,23]],"date-time":"2007-07-23T16:13:46Z","timestamp":1185207226000},"page":"i80-i86","source":"Crossref","is-referenced-by-count":8,"title":["A physical model for tiling array analysis"],"prefix":"10.1093","volume":"23","author":[{"given":"Ho-Ryun","family":"Chung","sequence":"first","affiliation":[{"name":"Max-Planck-Institut f\u00fcr molekulare Genetik, Ihnestrasse 63-73, 14195 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dennis","family":"Kostka","sequence":"additional","affiliation":[{"name":"Max-Planck-Institut f\u00fcr molekulare Genetik, Ihnestrasse 63-73, 14195 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Vingron","sequence":"additional","affiliation":[{"name":"Max-Planck-Institut f\u00fcr molekulare Genetik, Ihnestrasse 63-73, 14195 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,7,1]]},"reference":[{"key":"2023062708513419300_B1","first-page":"28","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers","volume":"2","author":"Bailey","year":"1994","journal-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol"},{"key":"2023062708513419300_B2","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1101\/gr.4887606","article-title":"Unbiased location analysis of e2f1-binding sites suggests a widespread role for e2f1 in the human genome","volume":"16","author":"Bieda","year":"2006","journal-title":"Genome Res"},{"key":"2023062708513419300_B3","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":"2023062708513419300_B4","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res"},{"key":"2023062708513419300_B5","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/ng0492-45","article-title":"Definition of a consensus binding site for p53","volume":"1","author":"elDeiry","year":"1992","journal-title":"Nat Genet"},{"key":"2023062708513419300_B6","doi-asserted-by":"crossref","first-page":"1372","DOI":"10.1093\/nar\/gkh299","article-title":"Detection of functional dna motifs via statistical over-representation","volume":"32","author":"Frith","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023062708513419300_B7","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":"2023062708513419300_B8","doi-asserted-by":"crossref","first-page":"1962","DOI":"10.1093\/nar\/gkg283","article-title":"Absolute mrna concentrations from sequence-specific calibration of oligonucleotide arrays","volume":"31","author":"Hekstra","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2023062708513419300_B9","doi-asserted-by":"crossref","first-page":"3629","DOI":"10.1093\/bioinformatics\/bti593","article-title":"Tilemap: create chromosomal map of tiling array hybridizations","volume":"21","author":"Ji","year":"2005","journal-title":"Bioinformatics"},{"key":"2023062708513419300_B10","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. Natl Acad. Sci. USA"},{"key":"2023062708513419300_B11","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1089\/cmb.2006.13.579","article-title":"Multiple testing methods for chip-chip high density oligonucleotide array data","volume":"13","author":"Keles","year":"2006","journal-title":"J. Comput. Biol"},{"issue":"Suppl. 1","key":"2023062708513419300_B12","doi-asserted-by":"crossref","first-page":"i274","DOI":"10.1093\/bioinformatics\/bti1046","article-title":"A hidden markov model for analyzing chip-chip experiments on genome tiling arrays and its application to p53 binding sequences","volume":"21","author":"Li","year":"2005","journal-title":"Bioinformatics"},{"key":"2023062708513419300_B13","doi-asserted-by":"crossref","first-page":"12247","DOI":"10.1073\/pnas.2135255100","article-title":"Distribution of nf-kappab-binding sites across human chromosome 22","volume":"100","author":"Martone","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023062708513419300_B14","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1093\/bioinformatics\/btl565","article-title":"Predicting transcription factor affinities to DNA from a biophysical model","volume":"23","author":"Roider","year":"2007","journal-title":"Bioinformatics"},{"key":"2023062708513419300_B15","doi-asserted-by":"crossref","first-page":"D91","DOI":"10.1093\/nar\/gkh012","article-title":"Jaspar: an open-access database for eukaryotic transcription factor binding profiles","volume":"32","author":"Sandelin","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023062708513419300_B16","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1073\/pnas.95.4.1460","article-title":"A unified view of polymer, dumbbell, and oligonucleotide dna nearest-neighbor thermodynamics","volume":"95","author":"SantaLucia","year":"1998","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023062708513419300_B17","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1089\/cmb.2005.12.882","article-title":"Stochastic models inspired by hybridization theory for short oligonucleotide arrays","volume":"12","author":"Wu","year":"2005","journal-title":"J. Comput. Biol"},{"key":"2023062708513419300_B18","doi-asserted-by":"crossref","first-page":"17834","DOI":"10.1073\/pnas.0604129103","article-title":"Global mapping of c-myc binding sites and target gene networks in human b cells","volume":"103","author":"Zeller","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023062708513419300_B19","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1038\/nbt836","article-title":"A model of molecular interactions on short oligonucleotide microarrays","volume":"21","author":"Zhang","year":"2003","journal-title":"Nat. Biotechnol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/13\/i80\/50718058\/bioinformatics_23_13_i80.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/13\/i80\/50718058\/bioinformatics_23_13_i80.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T08:53:58Z","timestamp":1687856038000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/13\/i80\/225638"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,7,1]]},"references-count":19,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2007,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm167","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,7]]},"published":{"date-parts":[[2007,7,1]]}}}