Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium
dc.contributor.author | Wang, Jie | |
dc.contributor.author | Zhuang, Jiali | |
dc.contributor.author | Iyer, Sowmya | |
dc.contributor.author | Lin, Xinying | |
dc.contributor.author | Greven, Melissa C. | |
dc.contributor.author | Kim, Bong-Hyun | |
dc.contributor.author | Moore, Jill | |
dc.contributor.author | Pierce, Brian G. | |
dc.contributor.author | Dong, Xianjun | |
dc.contributor.author | Virgil, Daniel | |
dc.contributor.author | Birney, Ewan | |
dc.contributor.author | Hung, Jui-Hung | |
dc.contributor.author | Weng, Zhiping | |
dc.date | 2022-08-11T08:07:59.000 | |
dc.date.accessioned | 2022-08-23T15:38:15Z | |
dc.date.available | 2022-08-23T15:38:15Z | |
dc.date.issued | 2013-01-01 | |
dc.date.submitted | 2013-02-22 | |
dc.identifier.citation | Nucleic 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.issn | 0305-1048 (Linking) | |
dc.identifier.doi | 10.1093/nar/gks1221 | |
dc.identifier.pmid | 23203885 | |
dc.identifier.uri | http://hdl.handle.net/20.500.14038/25897 | |
dc.description.abstract | 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. | |
dc.language.iso | en_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.subject | Databases, Genetic | |
dc.subject | Regulatory Elements, Transcriptional | |
dc.subject | Transcription Factors | |
dc.subject | Biochemistry, Biophysics, and Structural Biology | |
dc.subject | Bioinformatics | |
dc.subject | Computational Biology | |
dc.subject | Systems Biology | |
dc.title | Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium | |
dc.type | Journal Article | |
dc.source.journaltitle | Nucleic acids research | |
dc.source.volume | 41 | |
dc.source.issue | Database issue | |
dc.identifier.legacyfulltext | https://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=1003&context=bioinformatics_pubs&unstamped=1 | |
dc.identifier.legacycoverpage | https://escholarship.umassmed.edu/bioinformatics_pubs/4 | |
dc.identifier.contextkey | 3761385 | |
refterms.dateFOA | 2022-08-23T15:38:15Z | |
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.submissionpath | bioinformatics_pubs/4 | |
dc.contributor.department | Program in Bioinformatics and Integrative Biology | |
dc.contributor.department | Department of Biochemistry and Molecular Pharmacology | |
dc.source.pages | D171-6 |