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HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

Ivan V. Kulakovskiy, Yulia A. Medvedeva, Ulf Schaefer, Artem S. Kasianov, Ilya E. Vorontsov, Vladimir B. Bajic, Vsevolod J. Makeev
2012 Nucleic Acids Research  
Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks.  ...  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  ...  Conflict of interest statement. None declared. FUNDING  ... 
doi:10.1093/nar/gks1089 pmid:23175603 pmcid:PMC3531053 fatcat:eawcgj6w6nhlrhlfjydkvyl32i

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

Ivan V. Kulakovskiy, Ilya E. Vorontsov, Ivan S. Yevshin, Anastasiia V. Soboleva, Artem S. Kasianov, Haitham Ashoor, Wail Ba-alawi, Vladimir B. Bajic, Yulia A. Medvedeva, Fedor A. Kolpakov, Vsevolod J. Makeev
2015 Nucleic Acids Research  
Models of transcription factor (TF) binding sites provide a basis for a wide spectrum of studies in regulatory genomics, from reconstruction of regulatory networks to functional annotation of transcripts  ...  HOCOMOCO now provides position weight matrix (PWM) models for binding sites of 601 human TFs and, in addition, PWMs for 396 mouse TFs.  ...  HOCOMOCO comprises binding models for 601 human TFs, which is less than half of all known human transcription factors (8) .  ... 
doi:10.1093/nar/gkv1249 pmid:26586801 pmcid:PMC4702883 fatcat:ghirymw7vjf7zgixzc5bmzvtka

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

Ivan V Kulakovskiy, Ilya E Vorontsov, Ivan S Yevshin, Ruslan N Sharipov, Alla D Fedorova, Eugene I Rumynskiy, Yulia A Medvedeva, Arturo Magana-Mora, Vladimir B Bajic, Dmitry A Papatsenko, Fedor A Kolpakov, Vsevolod J Makeev
2017 Nucleic Acids Research  
We present a major update of the HOCOMOCO collection that consists of patterns describing DNA binding specificities for human and mouse transcription factors.  ...  In this release, we profited from a nearly doubled volume of published in vivo experiments on transcription factor (TF) binding to expand the repertoire of binding models, replace low-quality models previously  ...  ACKNOWLEDGEMENTS We thank Evolutionary Genomics Laboratory, Faculty of Bioengineering and Bioinformatics (Lomonosov Moscow State University) and personally Prof. A.S.  ... 
doi:10.1093/nar/gkx1106 pmid:29140464 pmcid:PMC5753240 fatcat:m4st2l3jnbdwhi3heo4rz7tcum

GTRD: a database on gene transcription regulation—2019 update

Ivan Yevshin, Ruslan Sharipov, Semyon Kolmykov, Yury Kondrakhin, Fedor Kolpakov
2018 Nucleic Acids Research  
The current version of the Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org) contains information about: (i) transcription factor binding sites (TFBSs) and transcription coactivators  ...  weight matrices from the HOCOMOCO database.  ...  database HOCOMOCO (http://hocomoco11.autosome. ru/)--HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO)--is one of the biggest collections of motifs for the prediction of TFBSs (40) for human and mouse  ... 
doi:10.1093/nar/gky1128 pmid:30445619 pmcid:PMC6323985 fatcat:has6jvpv2jcedk4kh637qnyf4y

AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

Hui Hu, Ya-Ru Miao, Long-Hao Jia, Qing-Yang Yu, Qiong Zhang, An-Yuan Guo
2018 Nucleic Acids Research  
The Animal Transcription Factor DataBase (Ani-malTFDB) is a resource aimed to provide the most comprehensive and accurate information for animal transcription factors (TFs) and cofactors.  ...  human TFs; (v) TF expressions in 22 animal species; (vi) a TF binding site prediction tool to identify potential binding TFs for nucleotide sequences; (vii) a separate human TF database web interface (  ...  ACKNOWLEDGEMENTS We would like to thank colleagues in data production and database construction in groups of Ensembl, dbSNP, TCGA, TRANSFAC, JASPAR, HOCOMOCO and hTFtarget.  ... 
doi:10.1093/nar/gky822 pmid:30204897 fatcat:f6xyu6w46jb7lgog5do72e3mzy

TFutils: Data structures for transcription factor bioinformatics

Benjamin J. Stubbs, Shweta Gopaulakrishnan, Kimberly Glass, Nathalie Pochet, Celine Everaert, Benjamin Raby, Vincent Carey
2019 F1000Research  
TFutils provides catalogs of human TFs from three reference sources (CISBP, HOCOMOCO, and GO), a catalog of TF targets derived from MSigDb, and multiple approaches to enumerating TF binding sites.  ...  DNA transcription is intrinsically complex. Bioinformatic work with transcription factors (TFs) is complicated by a multiplicity of data resources and annotations.  ...  concept "DNA binding transcription factor activity"), CISBP (Catalog of Inferred Sequence Binding Preferences) (Weirauch et al. 2 ), HOCOMOCO (Homo sapiens Comprehensive Model Collection) (Kulakovskiy  ... 
doi:10.12688/f1000research.17976.1 pmid:31297189 pmcid:PMC6600865 fatcat:eyr6anix5rf37oidenqkuxghfe

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

Ivan Yevshin, Ruslan Sharipov, Tagir Valeev, Alexander Kel, Fedor Kolpakov
2016 Nucleic Acids Research  
GTRD--Gene Transcription Regulation Database (http://gtrd.biouml.org)--is a database of transcription factor binding sites (TFBSs) identified by ChIPseq experiments for human and mouse.  ...  binding sites predicted using position weight matrices from the HOCOMOCO database.  ...  ACKNOWLEDGEMENTS We thank Ivan Kulakovskiy and Vsevolod Makeev for collaboration between the HOCOMOCO and GTRD databases.  ... 
doi:10.1093/nar/gkw951 pmid:27924024 pmcid:PMC5210645 fatcat:33l6uk5nbvhsddnxktmeloff7m

DENdb: database of integrated human enhancers

Haitham Ashoor, Dimitrios Kleftogiannis, Aleksandar Radovanovic, Vladimir B. Bajic
2015 Database: The Journal of Biological Databases and Curation  
DENdb provides information about the overlap of enhancers with DNase I hypersensitive regions, ChIP-seq regions of a number of transcription factors and transcription factor binding motifs, means to explore  ...  Identification of enhancers, coupled with a comprehensive functional analysis of their properties, could improve our understanding of complex gene transcription mechanisms and gene regulation processes  ...  We mapped 426 (A-D quality) models from HOCOMOCO database to our integrated enhancers. We used FIMO (29) to map position weight matrix derived from binding sites for each TF to all enhancers.  ... 
doi:10.1093/database/bav085 pmid:26342387 pmcid:PMC4560934 fatcat:abvwh4qlkbdr3o7djtxklnpgia

hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets

Qiong Zhang, Wei Liu, Hong-Mei Zhang, Gui-Yan Xie, Ya-Ru Miao, Mengxuan Xia, An-Yuan Guo
2020 Genomics, Proteomics & Bioinformatics  
In this study, we constructed a database named hTFtarget, which integrated huge human TF target resources (7190 ChIP-seq samples of 659 TFs and high-confidence binding sites of 699 TFs) and epigenetic  ...  Transcription factors (TFs) as key regulators play crucial roles in biological processes.  ...  We also acknowledge the funding from the National Natural Science Foundation of China (Grant Nos. 31822030  ... 
doi:10.1016/j.gpb.2019.09.006 pmid:32858223 pmcid:PMC7647694 fatcat:4cw2pwvl3rcvxfgfqznqgudk5u

hTFtarget: a comprehensive database for regulations of human transcription factors and their targets [article]

Qiong Zhang
2019 bioRxiv   pre-print
In this study, we constructed a database named hTFtarget, which integrated huge human TF target resources (7,190 ChIP-Seq samples of 659 TFs and high confident TF binding sites of 699 TFs) and epigenetic  ...  Transcription factors (TFs) as key regulators play crucial roles in biological processes.  ...  ACKNOWLEDGEMENTS We would like to thank colleagues in groups of Ensembl, GEO, SRA, ENCODE, All rights reserved. No reuse allowed without permission.  ... 
doi:10.1101/843656 fatcat:zaqpc5njofabflz2vg7nhjciiq

Factorbook: an Updated Catalog of Transcription Factor Motifs and Candidate Regulatory Motif Sites [article]

Henry E Pratt, Gregory R Andrews, Nishigandha Phalke, Michael J Purcaro, Arjan G van der Velde, Jill E Moore, Zhiping Weng
2021 biorxiv/medrxiv   pre-print
of candidate cis-regulatory elements to annotate a comprehensive collection of genome-wide candidate TF binding sites.  ...  The human genome contains roughly 1,600 transcription factors (TFs), DNA-binding proteins recognizing characteristic sequence motifs to exert regulatory effects on gene expression.  ...  Genomic visualization of motifs and TF binding sites Human interaction remains essential in interpreting the biological significance of transcription factor motifs and regulatory elements.  ... 
doi:10.1101/2021.10.11.463518 fatcat:qs5mfzelkvfaddaqazygddfsna

TFutils: Data structures for transcription factor bioinformatics

Benjamin J. Stubbs, Shweta Gopaulakrishnan, Kimberly Glass, Nathalie Pochet, Celine Everaert, Benjamin Raby, Vincent Carey
2019 F1000Research  
TFutils provides catalogs of human TFs from three reference sources (CISBP, HOCOMOCO, and GO), a catalog of TF targets derived from MSigDb, and multiple approaches to enumerating TF binding sites, including  ...  DNA transcription is intrinsically complex. Bioinformatic work with transcription factors (TFs) is complicated by a multiplicity of data resources and annotations.  ...  The authors present TFutils, a Bioconductor package for analyze TFs and their binding sites. TFutils combines information and analysis capabilities from several popular sources into one interface.  ... 
doi:10.12688/f1000research.17976.2 fatcat:jfr3qi7xpfa6tnp574bme2hlae

Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

Tanvir Alam, Yulia A. Medvedeva, Hui Jia, James B. Brown, Leonard Lipovich, Vladimir B. Bajic, Roberto Mantovani
2014 PLoS ONE  
We report a specific signature of promoter-proximal transcriptional regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS).  ...  TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors.  ...  Transcription factor binding sites (TFBSs) enrichment We predicted TFBSs using 426 position weight matrices (PWMs) for 401 human TFs from the HOCOMOCO [33] database (v.8) (http://www.cbrc.kaust.edu.sa  ... 
doi:10.1371/journal.pone.0109443 pmid:25275320 pmcid:PMC4183604 fatcat:fkoggsz76jhwdl6szt7vheugma

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Giovanna Ambrosini, Ilya Vorontsov, Dmitry Penzar, Romain Groux, Oriol Fornes, Daria D. Nikolaeva, Benoit Ballester, Jan Grau, Ivo Grosse, Vsevolod Makeev, Ivan Kulakovskiy, Philipp Bucher
2020 Genome Biology  
Positional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities.  ...  Here we report results from all-against-all benchmarking of PWM models for DNA binding sites of human TFs on a large compilation of in vitro (HT-SELEX, PBM) and in vivo (ChIP-seq) binding data.  ...  We thank members of the GRECO consortium, in particular Martin Kuiper, for the encouragement and support of this projects in the form of dedicated workshops of the GREEKC COST action.  ... 
doi:10.1186/s13059-020-01996-3 pmid:32393327 fatcat:paqghcw6jrazbizkn5itbf4rly

Multinomial Convolutions for Joint Modeling of Sequence Motifs and Enhancer Activities [article]

Minjun Park, Salvi Singh, Francisco Jose Grisanti Canozo, Md Abul Hassan Samee
2020 bioRxiv   pre-print
MuSeAM utilizes multinomial convolutions that directly model sequence-specific motifs of protein-DNA binding.  ...  Massively parallel reporter assays (MPRAs) have enabled the study of transcriptional regulatory mechanisms at an unprecedented scale and with high quantitative resolution.  ...  Motif Databases To compare the MuSeAM motifs against currently known motifs, we used motifs from the HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO)-v11 [24] database of transcription factor binding  ... 
doi:10.1101/2020.07.28.224212 fatcat:f4frljimvzhvba3xp7cwpm6tlm
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