Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology
Medical Subject Headings
Databases, Genetic; Regulatory Elements, Transcriptional; Transcription Factors
Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Computational Biology | Systems Biology
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.
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Citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. doi: 10.1093/nar/gks1221. Link to article on publisher's site
Wang, Jie; Zhuang, Jiali; Iyer, Sowmya; Lin, Xinying; Greven, Melissa C.; Kim, Bong-Hyun; Moore, Jill; Pierce, Brian G.; Dong, Xianjun; Virgil, Daniel; Birney, Ewan; Hung, Jui-Hung; and Weng, Zhiping, "Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium" (2013). Program in Bioinformatics and Integrative Biology Publications and Presentations. Paper 4.