title: Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.
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.
authors.affiliation: Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.forename: Jiali
authors.initials: J
authors.lastname: Zhuang
authors.forename: Sowmya
authors.initials: S
authors.lastname: Iyer
authors.forename: Xin-Ying
authors.initials: XY
authors.lastname: Lin
authors.forename: Melissa C
authors.initials: MC
authors.lastname: Greven
authors.forename: Bong-Hyun
authors.initials: BH
authors.lastname: Kim
authors.forename: Jill
authors.initials: J
authors.lastname: Moore
authors.forename: Brian G
authors.initials: BG
authors.lastname: Pierce
authors.forename: Xianjun
authors.initials: X
authors.lastname: Dong
authors.forename: Daniel
authors.initials: D
authors.lastname: Virgil
authors.forename: Ewan
authors.initials: E
authors.lastname: Birney
authors.forename: Jui-Hung
authors.initials: JH
authors.lastname: Hung
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
mesh_terms: D001665:Binding Sites; D002460:Cell Line; D047369:Chromatin Immunoprecipitation; D030541:Databases, Genetic; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones; D006801:Humans; D020407:Internet; D009707:Nucleosomes / Q000378:metabolism; D059372:Nucleotide Motifs; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D006657:Histones; D009707:Nucleosomes; D014157:Transcription Factors