Factorbook: an Updated Catalog of Transcription Factor Motifs and Candidate Regulatory Motif Sites [preprint]
Authors
Pratt, Henry EAndrews, Gregory
Phalke, Nishigandha
Purcaro, Michael J.
van der Velde, Arjan
Moore, Jill E.
Weng, Zhiping
UMass Chan Affiliations
Graduate School of Biomedical SciencesProgram in Bioinformatics and Integrative Biology
Document Type
PreprintPublication Date
2021-10-12Keywords
BioinformaticsFactorbook
transcription factors
ENCODE
Amino Acids, Peptides, and Proteins
Bioinformatics
Computational Biology
Metadata
Show full item recordAbstract
The human genome contains roughly 1,600 transcription factors (TFs) (1), DNA-binding proteins recognizing characteristic sequence motifs to exert regulatory effects on gene expression. The binding specificities of these factors have been profiled both in vitro, using techniques such as HT-SELEX (2), and in vivo, using techniques including ChIP-seq (3, 4). We previously developed Factorbook, a TF-centric database of annotations, motifs, and integrative analyses based on ChIP-seq data from Phase II of the ENCODE Project. Here we present an update to Factorbook which significantly expands the breadth of cell type and TF coverage. The update includes an expanded motif catalog derived from thousands of ENCODE Phase II and III ChIP-seq experiments and HT-SELEX experiments; this motif catalog is integrated with the ENCODE registry of candidate cis-regulatory elements to annotate a comprehensive collection of genome-wide candidate TF binding sites. The database also offers novel tools for applying the motif models within machine learning frameworks and using these models for integrative analysis, including annotation of variants and disease and trait heritability. We will continue to expand the resource as ENCODE Phase IV data are released.Source
bioRxiv 2021.10.11.463518; doi: https://doi.org/10.1101/2021.10.11.463518. Link to preprint on bioRxiv.
DOI
10.1101/2021.10.11.463518Permanent Link to this Item
http://hdl.handle.net/20.500.14038/29887Notes
This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.
Related Resources
Now published in Nucleic Acids Research doi: 10.1093/nar/gkab1039
Rights
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.Distribution License
http://creativecommons.org/licenses/by-nc/4.0/ae974a485f413a2113503eed53cd6c53
10.1101/2021.10.11.463518
Scopus Count
Except where otherwise noted, this item's license is described as The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.