Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.

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TitleFactorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.
Publication TypeJournal Article
Year of Publication2013
AuthorsWang, J, Zhuang, J, Iyer, S, Lin, X-Y, Greven, MC, Kim, B-H, Moore, J, Pierce, BG, Dong, X, Virgil, D, Birney, E, Hung, J-H, Weng, Z
JournalNucleic Acids Res
Volume41
IssueDatabase issue
PaginationD171-6
Date Published2013 Jan
ISSN1362-4962
KeywordsBinding Sites, Cell Line, Chromatin Immunoprecipitation, Databases, Genetic, High-Throughput Nucleotide Sequencing, Histones, Humans, Internet, Nucleosomes, Nucleotide Motifs, Regulatory Elements, Transcriptional, Sequence Analysis, DNA, Transcription Factors
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.

DOI10.1093/nar/gks1221
Alternate JournalNucleic Acids Res.
PubMed ID23203885
PubMed Central IDPMC3531197
Grant ListU01 HG004695 / HG / NHGRI NIH HHS / United States
U41 HG007000 / HG / NHGRI NIH HHS / United States
U41 HG007000 / HG / NHGRI NIH HHS / United States