{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T05:22:19Z","timestamp":1674883339323},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Cellular processes are controlled, directly or indirectly, by the binding of hundreds of different DNA binding factors (DBFs) to the genome. One key to deeper understanding of the cell is discovering where, when and how strongly these DBFs bind to the DNA sequence. Direct measurement of DBF binding sites (BSs; e.g. through ChIP-Chip or ChIP-Seq experiments) is expensive, noisy and not available for every DBF in every cell type. Naive and most existing computational approaches to detecting which DBFs bind in a set of genomic regions of interest often perform poorly, due to the high false discovery rates and restrictive requirements for prior knowledge.<\/jats:p>\n               <jats:p>Results: We develop SparScape, a penalized Bayesian method for identifying DBFs active in the considered regions and predicting a joint probabilistic binding landscape. Using a sparsity-inducing penalization, SparScape is able to select a small subset of DBFs with enriched BSs in a set of DNA sequences from a much larger candidate set. This substantially reduces the false positives in prediction of BSs. Analysis of ChIP-Seq data in mouse embryonic stem cells and simulated data show that SparScape dramatically outperforms the naive motif scanning method and the comparable computational approaches in terms of DBF identification and BS prediction.<\/jats:p>\n               <jats:p>Availability and implementation: SparScape is implemented in C++ with OpenMP (optional at compilation) and is freely available at \u2018www.stat.ucla.edu\/\u223czhou\/Software.html\u2019 for academic use.<\/jats:p>\n               <jats:p>Contact: \u00a0zhou@stat.ucla.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt585","type":"journal-article","created":{"date-parts":[[2013,10,11]],"date-time":"2013-10-11T16:14:08Z","timestamp":1381508048000},"page":"636-643","source":"Crossref","is-referenced-by-count":3,"title":["A penalized Bayesian approach to predicting sparse protein\u2013DNA binding landscapes"],"prefix":"10.1093","volume":"30","author":[{"given":"Matthew","family":"Levinson","sequence":"first","affiliation":[{"name":"Department of Statistics, University of California, Los Angeles, CA 90095, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qing","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of California, Los Angeles, CA 90095, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,10,9]]},"reference":[{"key":"2023012710433610000_btt585-B1","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1093\/bioinformatics\/btr695","article-title":"MotEvo: integrated bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences","volume":"28","author":"Arnold","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012710433610000_btt585-B2","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1038\/nbt1246","article-title":"Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities","volume":"24","author":"Berger","year":"2006","journal-title":"Nat. Biotechnol."},{"key":"2023012710433610000_btt585-B3","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/j.cell.2008.04.043","article-title":"Integration of external signaling pathways with the core transcriptional network in embryonic stem cells","volume":"133","author":"Chen","year":"2008","journal-title":"Cell"},{"key":"2023012710433610000_btt585-B4","doi-asserted-by":"crossref","first-page":"2381","DOI":"10.1101\/gr.1271603","article-title":"A biophysical approach to transcription factor binding site discovery","volume":"13","author":"Djordjevic","year":"2003","journal-title":"Genome Res."},{"key":"2023012710433610000_btt585-B5","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1101\/gr.096305.109","article-title":"Integrating multiple evidence sources to predict transcription factor binding in the human genome","volume":"20","author":"Ernst","year":"2010","journal-title":"Genome Res."},{"key":"2023012710433610000_btt585-B6","doi-asserted-by":"crossref","first-page":"1705","DOI":"10.1002\/stem.736","article-title":"Zfp281 functions as a transcriptional repressor for pluripotency of mouse embryonic stem cells","volume":"29","author":"Fidalgo","year":"2011","journal-title":"Stem Cells"},{"key":"2023012710433610000_btt585-B7","doi-asserted-by":"crossref","first-page":"e141","DOI":"10.1093\/bioinformatics\/btl223","article-title":"Statistical mechanical modeling of genome-wide transcription factor occupancy data by matrixreduce","volume":"22","author":"Foat","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012710433610000_btt585-B8","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1080\/01621459.2012.754359","article-title":"Learning sparse causal gaussian networks with experimental intervention: regularization and coordinate descent","volume":"108","author":"Fu","year":"2013","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012710433610000_btt585-B9","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1007\/s10142-007-0072-5","article-title":"Inactivation of the 3-phosphoglycerate dehydrogenase gene in mice: changes in gene expression and associated regulatory networks resulting from serine deficiency","volume":"8","author":"Furuya","year":"2008","journal-title":"Funct. Integr. Genomics"},{"key":"2023012710433610000_btt585-B10","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1002\/stem.652","article-title":"Differential recruitment of methyl CpG-binding domain factors and dna methyltransferases by the orphan receptor germ cell nuclear factor initiates the repression and silencing of oct4","volume":"29","author":"Gu","year":"2011","journal-title":"Stem Cells"},{"key":"2023012710433610000_btt585-B11","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1198\/016214503388619094","article-title":"Discovery of conserved sequence patterns using a stochastics dictionary model","volume":"98","author":"Gupta","year":"2003","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012710433610000_btt585-B12","doi-asserted-by":"crossref","first-page":"e8155","DOI":"10.1371\/journal.pone.0008155","article-title":"A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data","volume":"4","author":"He","year":"2009","journal-title":"PLoS One"},{"key":"2023012710433610000_btt585-B13","doi-asserted-by":"crossref","first-page":"e1000935","DOI":"10.1371\/journal.pcbi.1000935","article-title":"Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression","volume":"6","author":"He","year":"2010","journal-title":"PLoS Comput. Biol."},{"key":"2023012710433610000_btt585-B14","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1177\/1947601910379012","article-title":"Transcriptional repression: the dark side of myc","volume":"1","author":"Herkert","year":"2010","journal-title":"Genes Cancer"},{"key":"2023012710433610000_btt585-B15","doi-asserted-by":"crossref","first-page":"1552","DOI":"10.1002\/glia.20761","article-title":"Negative regulation of myelination: relevance for development, injury, and demyelinating disease","volume":"56","author":"Jessen","year":"2008","journal-title":"Glia"},{"key":"2023012710433610000_btt585-B16","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1038\/nature07667","article-title":"The DNA-encoded nucleosome organization of a eukaryotic genome","volume":"458","author":"Kaplan","year":"2009","journal-title":"Nature"},{"key":"2023012710433610000_btt585-B17","doi-asserted-by":"crossref","first-page":"e1001290","DOI":"10.1371\/journal.pgen.1001290","article-title":"Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early drosophila development","volume":"7","author":"Kaplan","year":"2011","journal-title":"PLoS Genet."},{"key":"2023012710433610000_btt585-B18","doi-asserted-by":"crossref","first-page":"3941","DOI":"10.1242\/jcs.024802","article-title":"Myc increases self-renewal in neural progenitor cells through miz-1","volume":"121","author":"Kerosuo","year":"2008","journal-title":"J. Cell Sci."},{"key":"2023012710433610000_btt585-B19","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1038\/nbt.1508","article-title":"Design and analysis of chip-seq experiments for dna-binding proteins","volume":"26","author":"Kharchenko","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"2023012710433610000_btt585-B20","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1016\/j.cell.2008.02.039","article-title":"An extended transcriptional network for pluripotency of embryonic stem cells","volume":"132","author":"Kim","year":"2008","journal-title":"Cell"},{"key":"2023012710433610000_btt585-B21","doi-asserted-by":"crossref","first-page":"e146","DOI":"10.1093\/nar\/gkp789","article-title":"A protein-protein interaction guided method for competitive transcription factor binding improves target predictions","volume":"37","author":"Laurila","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012710433610000_btt585-B22","doi-asserted-by":"crossref","first-page":"1334","DOI":"10.1101\/gr.127191.111","article-title":"Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks","volume":"22","author":"Marbach","year":"2012","journal-title":"Genome Res."},{"key":"2023012710433610000_btt585-B23","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1186\/1471-2164-10-327","article-title":"Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells","volume":"10","author":"Mason","year":"2009","journal-title":"BMC Genomics"},{"key":"2023012710433610000_btt585-B24","doi-asserted-by":"crossref","first-page":"2826","DOI":"10.1093\/bioinformatics\/btq546","article-title":"Identification of context-dependent motifs by contrasting chip binding data","volume":"26","author":"Mason","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012710433610000_btt585-B25","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1093\/nar\/gkg108","article-title":"TRANSFAC: transcriptional regulation, from patterns to profiles","volume":"31","author":"Matys","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012710433610000_btt585-B26","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1101\/gad.1032503","article-title":"c-MYC apoptotic function is mediated by NRF-1 target genes","volume":"17","author":"Morrish","year":"2002","journal-title":"Gene Dev."},{"key":"2023012710433610000_btt585-B27","doi-asserted-by":"crossref","first-page":"e215","DOI":"10.1371\/journal.pcbi.0030215","article-title":"A nucleosome-guided map of transcription factor binding sites in yeast","volume":"3","author":"Narlikar","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"2023012710433610000_btt585-B28","doi-asserted-by":"crossref","first-page":"2071","DOI":"10.1093\/bioinformatics\/btq405","article-title":"Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites","volume":"26","author":"Ramsey","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012710433610000_btt585-B29","doi-asserted-by":"crossref","first-page":"1480","DOI":"10.1101\/gr.088260.108","article-title":"Incorporating nucleosomes into thermodynamic models of transcription regulation","volume":"19","author":"Raveh-Sadka","year":"2009","journal-title":"Genome Res."},{"key":"2023012710433610000_btt585-B30","first-page":"414105","article-title":"Statistical-mechanical lattice models for protein-DNA binding in chromatin","volume":"22","author":"Teif","year":"2010","journal-title":"J. Phys: Condens. Matter"},{"key":"2023012710433610000_btt585-B31","doi-asserted-by":"crossref","first-page":"30285","DOI":"10.1074\/jbc.M704428200","article-title":"The RAS-dependent erf control of cell proliferation and differentiation is mediated by c-Myc repression","volume":"282","author":"Verykokakis","year":"2007","journal-title":"J. Biol. Chem."},{"key":"2023012710433610000_btt585-B32","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1038\/nature05284","article-title":"A protein interaction network for pluripotency of embryonic stem cells","volume":"444","author":"Wang","year":"2006","journal-title":"Nature"},{"key":"2023012710433610000_btt585-B33","doi-asserted-by":"crossref","first-page":"2101","DOI":"10.1101\/gr.093450.109","article-title":"An ensemble model of competitive multi-factor binding of the genome","volume":"19","author":"Wasson","year":"2009","journal-title":"Genome Res."},{"key":"2023012710433610000_btt585-B34","doi-asserted-by":"crossref","first-page":"R7","DOI":"10.1186\/gb-2010-11-1-r7","article-title":"Genome-wide prediction of transcription factor binding sites using an integrated model","volume":"11","author":"Won","year":"2010","journal-title":"Genome Biol."},{"key":"2023012710433610000_btt585-B35","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1089\/cmb.2009.0142","article-title":"On weight matrix and free energy models for sequence motif detection","volume":"17","author":"Zhou","year":"2010","journal-title":"J. Comput. Biol."},{"key":"2023012710433610000_btt585-B36","doi-asserted-by":"crossref","first-page":"12114","DOI":"10.1073\/pnas.0402858101","article-title":"CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling","volume":"101","author":"Zhou","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012710433610000_btt585-B37","doi-asserted-by":"crossref","first-page":"16438","DOI":"10.1073\/pnas.0701014104","article-title":"A gene regulatory network in mouse embryonic stem cells","volume":"104","author":"Zhou","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/5\/636\/48919504\/bioinformatics_30_5_636.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/5\/636\/48919504\/bioinformatics_30_5_636.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:04:56Z","timestamp":1674817496000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/5\/636\/246211"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,10,9]]},"references-count":37,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2014,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt585","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,3,1]]},"published":{"date-parts":[[2013,10,9]]}}}