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

Jie Wang, Jiali Zhuang, Sowmya Iyer, Xin Ying Lin, Melissa C. Greven, Bong Hyun Kim, Jill Moore, Brian G. Pierce, Xianjun Dong, Daniel Virgil, Ewan Birney, Jui-Hung Hung, Zhiping Weng*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

161 Scopus citations

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), micro-coccal 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.

Original languageEnglish
JournalNucleic acids research
Volume41
Issue numberD1
DOIs
StatePublished - 1 Jan 2013

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