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dc.contributor.authorWang, Jie
dc.contributor.authorZhuang, Jiali
dc.contributor.authorIyer, Sowmya
dc.contributor.authorLin, Xinying
dc.contributor.authorGreven, Melissa C.
dc.contributor.authorKim, Bong-Hyun
dc.contributor.authorMoore, Jill
dc.contributor.authorPierce, Brian G.
dc.contributor.authorDong, Xianjun
dc.contributor.authorVirgil, Daniel
dc.contributor.authorBirney, Ewan
dc.contributor.authorHung, Jui-Hung
dc.contributor.authorWeng, Zhiping
dc.date2022-08-11T08:07:59.000
dc.date.accessioned2022-08-23T15:38:15Z
dc.date.available2022-08-23T15:38:15Z
dc.date.issued2013-01-01
dc.date.submitted2013-02-22
dc.identifier.citationNucleic Acids Res. 2013 Jan;41(Database issue):D171-6. doi: 10.1093/nar/gks1221. <a href="http://dx.doi.org/10.1093/nar/gks1221">Link to article on publisher's site</a>
dc.identifier.issn0305-1048 (Linking)
dc.identifier.doi10.1093/nar/gks1221
dc.identifier.pmid23203885
dc.identifier.urihttp://hdl.handle.net/20.500.14038/25897
dc.description.abstractThe Encyclopedia of DNA Elements (ENCODE) consortium aims to identify all functional elements in the human genome including transcripts, transcriptional regulatory regions, along with their chromatin states and DNA methylation patterns. The ENCODE project generates data utilizing a variety of techniques that can enrich for regulatory regions, such as chromatin immunoprecipitation (ChIP), micrococcal nuclease (MNase) digestion and DNase I digestion, followed by deeply sequencing the resulting DNA. As part of the ENCODE project, we have developed a Web-accessible repository accessible at http://factorbook.org. In Wiki format, factorbook is a transcription factor (TF)-centric repository of all ENCODE ChIP-seq datasets on TF-binding regions, as well as the rich analysis results of these data. In the first release, factorbook contains 457 ChIP-seq datasets on 119 TFs in a number of human cell lines, the average profiles of histone modifications and nucleosome positioning around the TF-binding regions, sequence motifs enriched in the regions and the distance and orientation preferences between motif sites.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=23203885&dopt=Abstract">Link to Article in PubMed</a>
dc.rights© The Author(s) 2012. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.
dc.subjectDatabases, Genetic
dc.subjectRegulatory Elements, Transcriptional
dc.subjectTranscription Factors
dc.subjectBiochemistry, Biophysics, and Structural Biology
dc.subjectBioinformatics
dc.subjectComputational Biology
dc.subjectSystems Biology
dc.titleFactorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium
dc.typeJournal Article
dc.source.journaltitleNucleic acids research
dc.source.volume41
dc.source.issueDatabase issue
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=1003&amp;context=bioinformatics_pubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/bioinformatics_pubs/4
dc.identifier.contextkey3761385
refterms.dateFOA2022-08-23T15:38:15Z
html.description.abstract<p>The Encyclopedia of DNA Elements (ENCODE) consortium aims to identify all functional elements in the human genome including transcripts, transcriptional regulatory regions, along with their chromatin states and DNA methylation patterns. The ENCODE project generates data utilizing a variety of techniques that can enrich for regulatory regions, such as chromatin immunoprecipitation (ChIP), micrococcal nuclease (MNase) digestion and DNase I digestion, followed by deeply sequencing the resulting DNA. As part of the ENCODE project, we have developed a Web-accessible repository accessible at http://factorbook.org. In Wiki format, factorbook is a transcription factor (TF)-centric repository of all ENCODE ChIP-seq datasets on TF-binding regions, as well as the rich analysis results of these data. In the first release, factorbook contains 457 ChIP-seq datasets on 119 TFs in a number of human cell lines, the average profiles of histone modifications and nucleosome positioning around the TF-binding regions, sequence motifs enriched in the regions and the distance and orientation preferences between motif sites.</p>
dc.identifier.submissionpathbioinformatics_pubs/4
dc.contributor.departmentProgram in Bioinformatics and Integrative Biology
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.source.pagesD171-6


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