UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology



Document Type


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 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.

Rights and Permissions

Citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. doi: 10.1093/nar/gks1221. Link to article on publisher's site


© The Author(s) 2012. Published by Oxford University Press.

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Link to Article in PubMed


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