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JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

Anthony Mathelier, Oriol Fornes, David J. Arenillas, Chih-yu Chen, Grégoire Denay, Jessica Lee, Wenqiang Shi, Casper Shyr, Ge Tan, Rebecca Worsley-Hunt, Allen W. Zhang, François Parcy (+3 others)
2015 Nucleic Acids Research  
Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles.  ...  JASPAR (http://jaspar.genereg.net) is an openaccess database storing curated, non-redundant transcription factor (TF) binding profiles represent- ing transcription factor binding preferences as position  ...  Weirauch and Mihai Albu for sharing the TF profile inference code implemented in the CIS-BP website, and Roberto Solano and José Manuel Franco-Zorrilla for providing their PBM data.  ... 
doi:10.1093/nar/gkv1176 pmid:26531826 pmcid:PMC4702842 fatcat:dfyf2xpuprh4pg2udndeovgxrm

JASPAR RESTful API: accessing JASPAR data from any programming language [article]

Aziz Khan, Anthony Mathelier
2017 bioRxiv   pre-print
JASPAR is a widely used open-access database of curated, non-redundant transcription factor binding profiles.  ...  Further, it provides an endpoint to infer the TF binding profile(s) likely bound by a given DNA binding domain protein sequence.  ...  Acknowledgements We thank all JASPAR collaborators for their useful suggestions and testing the API, and Georgios Magklaras for IT support.  ... 
doi:10.1101/160184 fatcat:u46ntu3olrfu7bcllo7m6fyrge

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Aziz Khan, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime A Castro-Mondragon, Robin van der Lee, Adrien Bessy, Jeanne Chèneby, Shubhada R Kulkarni, Ge Tan, Damir Baranasic, David J Arenillas (+7 others)
2017 Nucleic Acids Research  
ACKNOWLEDGEMENTS We thank the scientific community for performing experimental assays of TF-DNA interactions and for publicly releasing the data.  ...  We thank José Manuel Franco for sharing the plant PBM data, Jens De Ceukeleire for help with plant ChIP-seq data processing and José Luis Villanueva-Cañas for sharing the Drosophila TFFMs prior to publication  ...  In this report, we describe the seventh release of JASPAR (8, (20) (21) (22) (23) (24) , which comes with a major expansion and update of the CORE collection of TF-binding profiles as PFMs and TFFMs.  ... 
doi:10.1093/nar/gkx1126 pmid:29140473 pmcid:PMC5753243 fatcat:bzfitmkui5e4fihzspdn2roula

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David Arenillas, Anthony Mathelier, Yulia A. Medvedeva, Andreas Lennartsson, Finn Drabløs (+13 others)
2016 Nucleic Acids Research  
Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FAN-TOM  ...  In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced.  ...  ACKNOWLEDGEMENTS The authors would like to thank all of the members in the FANTOM consortium for fruitful collaboration.  ... 
doi:10.1093/nar/gkw995 pmid:27794045 pmcid:PMC5210666 fatcat:5z6fqqnewbbi7a5mwaipsgmi44

MD-SVM: a novel SVM-based algorithm for the motif discovery of transcription factor binding sites

Jialu Hu, Jingru Wang, Jianan Lin, Tianwei Liu, Yuanke Zhong, Jie Liu, Yan Zheng, Yiqun Gao, Junhao He, Xuequn Shang
2019 BMC Bioinformatics  
Jaspar 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2016;44:110–5. 23.  ...  Jaspar, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res. 2008;36:102–6. 22.  ... 
doi:10.1186/s12859-019-2735-3 fatcat:5nxu74qsavcyhoyi36vgjhx6eq

The borders of cis-regulatory DNA sequences harbor the divergent transcription factor binding motifs in the human genome [article]

Jia-Hsin Huang, Ryan Shun-Yuen Kwan, Zing Tsung-Yeh Tsai, Huai-Kuang Tsai
2018 bioRxiv   pre-print
Changes in the cis-regulatory DNA sequences and transcription factor (TF) repertoires provide major sources that shape the gene regulatory evolution in eukaryotes.  ...  Here, we estimated the evolutionary divergence level of the TF binding motifs, and quantified their occurrences in the DNase I hypersensitive sites.  ...  the JASPAR 407 database and their MPI scores.  ... 
doi:10.1101/383182 fatcat:jw53u2iaxnhpvk3wxrukq4tpnu

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  ...  The update is based on the analysis of massive ChIP-Seq and HT-SELEX datasets, with the validation of the resulting models on in vivo data.  ...  D118 Nucleic Acids Research, 2016, Vol. 44, Database issue Figure 1 . 1 Overview of the HOCOMOCO update workflow.  ... 
doi:10.1093/nar/gkv1249 pmid:26586801 pmcid:PMC4702883 fatcat:ghirymw7vjf7zgixzc5bmzvtka

ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments

2019 Nucleic Acids Research  
ReMap (http://remap.univ-amu.fr) aims to provide the largest catalogs of high-quality regulatory regions resulting from a large-scale integrative analysis of hundreds of transcription factors and regulators  ...  The updated human atlas totalize 5798 datasets covering a total of 1135 transcriptional regulators (TRs) with a catalog of 165 million (M) peaks.  ...  This ReMap update comes with two unique Arabidopsis regulatory catalogues, one providing 372 transcription factors and general actors of the transcriptional machinery and a second catalogue of 33 of known  ... 
doi:10.1093/nar/gkz945 pmid:31665499 pmcid:PMC7145625 fatcat:n4ve2kjtk5grnmzihal2kqkxdy

Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci

Clint L. Miller, Milos Pjanic, Ting Wang, Trieu Nguyen, Ariella Cohain, Jonathan D. Lee, Ljubica Perisic, Ulf Hedin, Ramendra K. Kundu, Deshna Majmudar, Juyong B. Kim, Oliver Wang (+8 others)
2016 Nature Communications  
Coronary artery disease (CAD) is the leading cause of mortality and morbidity, driven by both genetic and environmental risk factors.  ...  A majority of these variants reside in non-coding regions and are co-inherited with hundreds of candidate regulatory variants, presenting a challenge to elucidate their functions.  ...  Acknowledgements We thank all members of the CARDIoGRAMplusC4D consortium for performing the 1000 Genomes analyses and all volunteers for participating in the association studies; William Greenleaf and  ... 
doi:10.1038/ncomms12092 pmid:27386823 pmcid:PMC4941121 fatcat:fymr7p57xvfrhbx437wjx4h5eu

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells [article]

Sebastian Pott
2016 bioRxiv   pre-print
In addition, scNOMe-seq provided high resolution of chromatin accessibility within individual loci which was exploited to detect footprints of CTCF binding events and to estimate the average nucleosome  ...  Gaining insights into the regulatory mechanisms that underlie the transcriptional variation observed between individual cells necessitates the development of methods that measure chromatin organization  ...  Chromatin 1 accessibility signal can vary along the length of a given DHSs due to binding of transcription 2 factors (Neph et al. 2012 ) and the specific position of a GpC within a DHS will thus affect  ... 
doi:10.1101/061739 fatcat:ry7vjeqcazavzl5mol2pwhuwxa

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types

Cory C. Funk, Alex M. Casella, Segun Jung, Matthew A. Richards, Alex Rodriguez, Paul Shannon, Rory Donovan-Maiye, Ben Heavner, Kyle Chard, Yukai Xiao, Gustavo Glusman, Nilufer Ertekin-Taner (+9 others)
2020 Cell Reports  
Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation.  ...  Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT.  ...  the footprint locations with motifs and motif-transcription factor mappings from JASPAR, HOCOMOCO, UniPROBE, and SwissRegulon.  ... 
doi:10.1016/j.celrep.2020.108029 pmid:32814038 pmcid:PMC7462736 fatcat:lnjt2ouxv5ag3ehjzvygmbwsqe

Occupancy maps of 208 chromatin-associated proteins in one human cell type

E. Christopher Partridge, Surya B. Chhetri, Jeremy W. Prokop, Ryne C. Ramaker, Camden S. Jansen, Say-Tar Goh, Mark Mackiewicz, Kimberly M. Newberry, Laurel A. Brandsmeier, Sarah K. Meadows, C. Luke Messer, Andrew A. Hardigan (+8 others)
2020 Nature  
The binding profiles of these CAPs form major groups associated predominantly with promoters or enhancers, or with both.  ...  However, only a minority of the more than 1,600 transcription factors encoded in the human genome has been assayed.  ...  Software Software listed above, described in the methods section of the manuscript, and on the ENCODE portal.  ... 
doi:10.1038/s41586-020-2023-4 pmid:32728244 fatcat:vhzfnqjerrerfjcp72rmp6chxq

Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks

Maud Fagny, Marieke Lydia Kuijjer, Maike Stam, Johann Joets, Olivier Turc, Julien Rozière, Stéphanie Pateyron, Anthony Venon, Clémentine Vitte
2021 Frontiers in Genetics  
Characterizing the transcription factors (TFs) and genes they connect, and the molecular functions underpinned is important to better characterize developmental processes.  ...  Nevertheless, identifying these target genes at a genome-wide level is challenging, particularly for large-genome species, where enhancers and target genes can be hundreds of kilobases away.  ...  To this end, we retrieved the MEME core plants position frequency matrix files corresponding to the binding sites of 489 transcription factors available in JASPAR database (accession October 31, 2019)  ... 
doi:10.3389/fgene.2020.606285 pmid:33505431 pmcid:PMC7834273 fatcat:w2wtinkzgnfsha6sq4fdpejh2y

Targeting the Non-Coding Genome for the Diagnosis of Disorders of Sex Development

Gabby Atlas, Rajini Sreenivasan, Andrew Sinclair
2021 Sexual Development  
We will review the available online tools and databases that can be used to refine regions with potential enhancer activity based on chromosomal accessibility, histone modifications, transcription factor  ...  The review concludes with a clinical update on the enhancers linked to DSD.  ...  Conflict of Interest Statement The authors have no conflicts of interest to declare. Funding Sources  ... 
doi:10.1159/000519238 pmid:34634785 fatcat:pdmgcllzi5fx7lypjnstcfhjca

Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi molting [article]

Alexandra Grote, Yichao Li, Canhui Liu, Denis Voronin, Adam Geber, Sara Lustigman, Thomas Unnasch, Lonnie Welch, Elodie Ghedin
2019 bioRxiv   pre-print
While whole genome sequences of parasitic worms are now available, very little is known about transcription factor (TF) binding sites and their cognate transcription factors that play a role in regulating  ...  We identified stage-specific TF binding motifs in B. malayi, with a particular focus on those potentially involved in the L3-L4 molt, a stage important for the establishment of infection in the mammalian  ...  JASPAR 2016: A Major Expansion and Update of the Open-Access 525 Database of Transcription Factor Binding Profiles. Nucleic Acids Research, 44 (D1) Table 1 : 1 RNA-Seq summary.  ... 
doi:10.1101/781930 fatcat:4mt2t2jfibew7ndiacg4swpto4
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