HOCOMOCO: A comprehensive collection of human transcription factor binding sites models
AuthorsKulakovskiy, Ivan V.
Medvedeva, Yulia A.
Kasianov, Artem S.
Vorontsov, Ilya E.
Bajic, Vladimir B.
Makeev, Vsevolod J.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Permanent link to this recordhttp://hdl.handle.net/10754/325453
MetadataShow full item record
AbstractTranscription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/ hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. The Author(s) 2012.
CitationKulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, et al. (2012) HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Research 41: D195-D202. doi:10.1093/nar/gks1089.
PublisherOxford University Press (OUP)
JournalNucleic Acids Research
PubMed Central IDPMC3531053
The following license files are associated with this item:
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact email@example.com.
- HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.
- Authors: Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ
- Issue date: 2016 Jan 4
- HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.
- Authors: Kulakovskiy IV, Vorontsov IE, Yevshin IS, Sharipov RN, Fedorova AD, Rumynskiy EI, Medvedeva YA, Magana-Mora A, Bajic VB, Papatsenko DA, Kolpakov FA, Makeev VJ
- Issue date: 2018 Jan 4
- Transcription Factor Information System (TFIS): A Tool for Detection of Transcription Factor Binding Sites.
- Authors: Narad P, Kumar A, Chakraborty A, Patni P, Sengupta A, Wadhwa G, Upadhyaya KC
- Issue date: 2017 Sep
- A novel method for improved accuracy of transcription factor binding site prediction.
- Authors: Khamis AM, Motwalli O, Oliva R, Jankovic BR, Medvedeva YA, Ashoor H, Essack M, Gao X, Bajic VB
- Issue date: 2018 Jul 6
- AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana.
- Authors: Bülow L, Brill Y, Hehl R
- Issue date: 2010
Showing items related by title, author, creator and subject.
Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulationMahas, Ahmed; Neal Stewart, C.; Mahfouz, Magdy M. (Biotechnology Advances, Elsevier BV, 2017-11-29) [Article]Genome editing has enabled broad advances and novel approaches in studies of gene function and structure; now, emerging methods aim to precisely engineer post-transcriptional processes. Developing precise, efficient molecular tools to alter the transcriptome holds great promise for biotechnology and synthetic biology applications. Different approaches have been employed for targeted degradation of RNA species in eukaryotes, but they lack programmability and versatility, thereby limiting their utility for diverse applications. The CRISPR/Cas9 system has been harnessed for genome editing in many eukaryotic species and, using a catalytically inactive Cas9 variant, the CRISPR/dCas9 system has been repurposed for transcriptional regulation. Recent studies have used other CRISPR/Cas systems for targeted RNA degradation and RNA-based manipulations. For example, Cas13a, a Type VI-A endonuclease, has been identified as an RNA-guided RNA ribonuclease and used for manipulation of RNA. Here, we discuss different modalities for targeted RNA interference with an emphasis on the potential applications of CRISPR/Cas systems as programmable transcriptional regulators for broad uses, including functional biology, biotechnology, and synthetic biology applications.
TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactionsSchmeier, Sebastian; Alam, Tanvir; Essack, Magbubah; Bajic, Vladimir B. (Nucleic Acids Research, Oxford University Press (OUP), 2016-10-17) [Article]Transcription factors (TFs) play a pivotal role in transcriptional regulation, making them crucial for cell survival and important biological functions. For the regulation of transcription, interactions of different regulatory proteins known as transcription co-factors (TcoFs) and TFs are essential in forming necessary protein complexes. Although TcoFs themselves do not bind DNA directly, their influence on transcriptional regulation and initiation, although indirect, has been shown to be significant, with the functionality of TFs strongly influenced by the presence of TcoFs. In the TcoF-DB v2 database, we collect information on TcoFs. In this article, we describe updates and improvements implemented in TcoF-DB v2. TcoF-DB v2 provides several new features that enables exploration of the roles of TcoFs. The content of the database has significantly expanded, and is enriched with information from Gene Ontology, biological pathways, diseases and molecular signatures. TcoF-DB v2 now includes many more TFs; has substantially increased the number of human TcoFs to 958, and now includes information on mouse (418 new TcoFs). TcoF-DB v2 enables the exploration of information on TcoFs and allows investigations into their influence on transcriptional regulation in humans and mice. TcoF-DB v2 can be accessed at http://tcofdb.org/.
RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factorsPiatek, Agnieszka Anna; Ali, Zahir; Baazim, Hatoon; Li, Lixin; Abulfaraj, Aala A.; Alshareef, Sahar; Aouida, Mustapha; Mahfouz, Magdy M. (Plant Biotechnology Journal, Wiley-Blackwell, 2014-11-14) [Article]Targeted genomic regulation is a powerful approach to accelerate trait discovery and development in agricultural biotechnology. Bacteria and archaea use clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) regulatory systems for adaptive molecular immunity against foreign nucleic acids introduced by invading phages and conjugative plasmids. The type II CRISPR/Cas system has been adapted for genome editing in many cell types and organisms. A recent study used the catalytically inactive Cas9 (dCas9) protein combined with guide-RNAs (gRNAs) as a DNA-targeting platform to modulate gene expression in bacterial, yeast, and human cells. Here, we modified this DNA-targeting platform for targeted transcriptional regulation in planta by developing chimeric dCas9-based transcriptional activators and repressors. To generate transcriptional activators, we fused the dCas9 C-terminus with the activation domains of EDLL and TAL effectors. To generate a transcriptional repressor, we fused the dCas9 C-terminus with the SRDX repression domain. Our data demonstrate that dCas9 fusion with the EDLL activation domain (dCas9:EDLL) and the TAL activation domain (dCas9:TAD), guided by gRNAs complementary to selected promoter elements, induce strong transcriptional activation on Bs3