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

By Jie Wang, Jiali Zhuang, Sowmya Iyer, Xin-Ying Lin, Melissa C. Greven, Bong-Hyun Kim, Jill E. Moore, Brian G. Pierce, Xianjun Dong, Daniel Virgil and 3 more. Nucleic Acids Res., 2012

297 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/47f4777fe2ee407374b1732acb03e5a56484ac4c

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Citations in the corpus

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution (2015, background): “Within each TF family, DNA binding specificity has also diverged considerably, with many families having 2–10 different subclasses displaying different primary binding specificities (Berger et al., 2008; Wei et al., 2010; Jolma et al., 2013).”
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants (2018, background): “To date, several databases have been developed to explore the occupancy landscapes of regulatory factors, such as, Cistrome DB (4), ReMap (5), Factorbook (6), GTRD (7), PlantTFDB (8), ChIPBase (9) and Expresso (10).”
The Human Transcription Factors. (2018, unknown): “Second, ChIP-seq can clearly detect indirect binding, which can lead to identification of motifs for proteins other than the one ChIPped (Wang et al., 2013; Worsley Hunt and Wasserman, 2014).”
hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets (2019, unknown): “Although several resources, such as ReMap [9], CistromeDB [10], Factorbook [11], ChIPBase [12], and TRRUST [13], were conducted to display the relationships between mammalian TFs and their targets, most of them indirectly provided evidence for TF–target regulations.”
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues (2020, unknown): “500 bp of the transcription start site of ACE2 (all in human studies, Figure S4B) (Gerstein et al., 2012; Matys et al., 2003; Wang et al., 2012; Wang et al., 2013).”
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis (2017, background): “However, we failed to identify any common binding pattern in vivo , and also, no common pattern could be found in Fac-torBook data as well (29).”
The UCSC Genome Browser database: 2015 update (2014, methodology): “Motif localizations from the Factorbook ENCODE annotation (36) are now displayed together with the ENCODE TF binding peak clusters.”
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity (2014, unknown): “, 2011), FactorBook (Wang et al., 2013), and data from 674 PBM experiments taken from other studies (compiled in UniPROBE) (Newburger and Bulyk, 2009).”