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JASPAR 2020: update of the open-access database of transcription factor binding profiles

2019 Nucleic Acids Research  
JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species  ...  JASPAR 2020 comes with a novel collection of unvalidated TF-binding profiles for which our curators did not find orthogonal supporting evidence in the literature.  ...  ACKNOWLEDGEMENTS We thank the user community for useful input and the scientific community for performing experimental assays of TF-DNA interactions and for publicly releasing the data.  ... 
doi:10.1093/nar/gkz1001 pmid:31701148 pmcid:PMC7145627 fatcat:hgljlnrtzjc2ppc2jvefvqy43i

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

UniBind: maps of high-confidence direct TF-DNA interactions across nine species [article]

Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime Abraham Castro-Mondragon, Anthony Mathelier
2020 bioRxiv   pre-print
Transcription factors (TFs) bind specifically to TF binding sites (TFBSs) at cis-regulatory regions to control transcription.  ...  All the data is provided to the community through the UniBind database that can be accessed through its web-interface (https://unibind.uio.no/), a dedicated RESTful API, and as genomic tracks.  ...  We thank Georgios Magklaras, Harold Gutch, and the NCMM IT team for their IT support, and Ingrid Kjelsvik for her administrative support. FUNDING  ... 
doi:10.1101/2020.11.17.384578 fatcat:ykszca24rrdchoo75xquo3eaoy

TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites

2019 Nucleic Acids Research  
TFBSshape (https://tfbsshape.usc.edu) is a motif database for analyzing structural profiles of transcription factor binding sites (TFBSs).  ...  The current expansion includes new entries from the most recent collections of transcription factors (TFs) from the JASPAR and UniPROBE databases, methylated TFBSs derived from in vitro high-throughput  ...  The current version of TFBSshape has been updated with the latest version of JASPAR 2020 (43) and with the continuously updated UniPROBE database (http://thebrain.bwh.harvard.edu/uniprobe/).  ... 
doi:10.1093/nar/gkz970 pmid:31665425 pmcid:PMC7145579 fatcat:sh4xvrr4nrg4xjlzk4x2odou6y

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  
Transcription factors (TFs) as key regulators play crucial roles in biological processes.  ...  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  ...  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

Evolution is in the details: Regulatory differences in modern human and Neandertal [article]

Harlan Barker, Seppo Parkkila, Martti Tolvanen
2020 bioRxiv   pre-print
Transcription factor (TF) proteins play a critical role in the regulation of eukaryote gene expression by sequence-specific binding to genomic locations known as transcription factor binding sites.  ...  We found significant differences in binding affinity for 86 transcription factors, groups of which are both highly expressed, and show correlation of expression, in immune cells and adult and developing  ...  The sequence is then scored using up to 575 JASPAR TFBS profiles.  ... 
doi:10.1101/2020.09.04.282749 fatcat:erqk6yskvfc2xk4ffk6gveilby

Machine learning for profile prediction in genomics

Jacob Schreiber, Ritambhara Singh
2021 Current Opinion in Chemical Biology  
, for example, histone modification, chromatin accessibility, or protein binding.  ...  In this review, we give an overview of the research works performing profile prediction, define two broad categories of profile prediction tasks, and discuss the types of scientific questions that can  ...  The figure in the paper is created using BioRender.com.  ... 
doi:10.1016/j.cbpa.2021.04.008 pmid:34107341 fatcat:x5sjjif2gjcwzmkzk6wl26cdja

UniBind: maps of high-confidence direct TF-DNA interactions across nine species

Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime Abraham Castro-Mondragon, Anthony Mathelier
2021 BMC Genomics  
Background Transcription factors (TFs) bind specifically to TF binding sites (TFBSs) at cis-regulatory regions to control transcription.  ...  All the data is provided to the community through the UniBind database that can be accessed through its web-interface (https://unibind.uio.no/), a dedicated RESTful API, and as genomic tracks.  ...  We thank Georgios Magklaras, Harold Gutch, and the NCMM IT team for their IT support, and Ingrid Kjelsvik for administrative support.  ... 
doi:10.1186/s12864-021-07760-6 pmid:34174819 fatcat:qvuntqdmjrh4zfj3unvt546gai

Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules

Mirko Ronzio, Federico Zambelli, Diletta Dolfini, Roberto Mantovani, Giulio Pavesi
2020 Frontiers in Genetics  
We show examples of its application to ENCODE data, that led to the identification of relevant regulatory modules composed of different factors, as well as the organization on DNA of the binding motifs  ...  As a consequence, it has become the de facto standard for studies on the regulation of transcription, and literally thousands of data sets for transcription factors and cofactors in different conditions  ...  Both already contain the latest release of the JASPAR database.  ... 
doi:10.3389/fgene.2020.00072 pmid:32153638 pmcid:PMC7046753 fatcat:evrqxbr5czftvdi465tjm6yuwe

ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments

Fayrouz Hammal, Pierre de Langen, Aurélie Bergon, Fabrice Lopez, Benoit Ballester
2021 Nucleic Acids Research  
, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators.  ...  The updated Human regulatory atlas includes 8103 datasets covering a total of 1210 transcriptional regulators (TRs) with a catalog of 182 million (M) peaks, while the updated Arabidopsis atlas reaches  ...  We would like to thank the JASPAR Team led by Anthony Mathelier from NCMM Norway for constant scientific feedback on the ReMap catalogues.  ... 
doi:10.1093/nar/gkab996 pmid:34751401 pmcid:PMC8728178 fatcat:k2zuwebeizfk5khhm5funirbfi

Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases

Joke Reumers, Lucia Conde, Ignacio Medina, Sebastian Maurer-Stroh, Joost Van Durme, Joaquin Dopazo, Frederic Rousseau, Joost Schymkowitz
2007 Nucleic Acids Research  
The combined database holds annotations for 4 965 073 regulatory as well as 133 505 coding human SNPs and 14 935 disease mutations, and phenotypic descriptions of 43 797 human proteins and is accessible  ...  The SNPeffect and PupaSuite databases are now synchronized to deliver annotations for both non-coding and coding SNP, as well as annotations for the SwissProt set of human disease mutations.  ...  Funding to pay the Open Access publication charges for this article was provided by a grant from the Federal Office of Scientific Affairs, Belgium (IUAP6/43).  ... 
doi:10.1093/nar/gkm979 pmid:18086700 pmcid:PMC2238831 fatcat:s2lyhit3bnga3lytnkv5itu6bi

Integrated regulatory models for inference of subtype‐specific susceptibilities in glioblastoma

Yunpeng Liu, Ning Shi, Aviv Regev, Shan He, Michael T Hemann
2020 Molecular Systems Biology  
Using a multilayer network consisting of 518 transcription factors (TFs), 10,733 target genes, and a signaling layer of 3,132 proteins, we were able to accurately identify differential regulatory activity  ...  We developed a modular computational pipeline, Integrative Modeling of Transcription Regulatory Interactions for Systematic Inference of Susceptibility in Cancer (inTRINSiC), to dissect subtype-specific  ...  Acknowledgements We thank Azucena Ramos, Catherine Koch, and James Dongjoo Ham for useful discussions and suggestions for the paper. This project was funded in part by the NCI (  ... 
doi:10.15252/msb.20209506 pmid:32974985 fatcat:d5f3sie66jakdpq53uxuexpxum

Interpretation of deep learning in genomics and epigenomics

Amlan Talukder, Clayton Barham, Xiaoman Li, Haiyan Hu
2020 Briefings in Bioinformatics  
We finally discuss the advantages and limitations of current interpretation approaches in the context of genomic and epigenomic studies. Contact:xiaoman@mail.ucf.edu, haihu@cs.ucf.edu  ...  We first describe state-of-the-art DNN interpretation methods in representative machine learning fields.  ...  A CNN model named Basenji was trained to predict cell-specific epigenetic and transcriptional profiles such as chromatin accessibility [47] .  ... 
doi:10.1093/bib/bbaa177 pmid:34020542 pmcid:PMC8138893 fatcat:4xlkzvvalrcipc2fcawu4kzigi

ULK1 and ULK2 are less redundant than previously thought: Computational analysis uncovers distinct regulation and functions of these autophagy induction proteins [article]

Amanda Demeter, Mari Carmen Romero-Mulero, Luca Csabai, Márton Ölbei, Padhmanand Sudhakar, Wilfried Haerty, Tamás Korcsmáros
2020 bioRxiv   pre-print
We identified three ULK1-specific and one ULK2-specific transcription factor binding sites, and eight sites shared by the regulatory region of both genes.  ...  Macroautophagy is initiated primarily by a complex containing ULK1 or ULK2 (two paralogs of the yeast Atg1 protein).  ...  JASPAR 2018: update of the open-access database of transcription 502 factor binding profiles and its web framework. Nucleic Acids Res. 46, D260-D266 503 (2018). 504 39. Türei, D. et al.  ... 
doi:10.1101/2020.02.27.967901 fatcat:gd4onv2q7jb6lkidorry23jju4

ATAC-seq with unique molecular identifiers improves quantification and footprinting [article]

Tao Zhu, Keyan Liao, Rongfang Zhou, Chunjiao Xia, Weibo Xie
2020 bioRxiv   pre-print
We demonstrate that UMI-ATAC-seq could more accurately quantify chromatin accessibility and significantly improve the sensitivity of identifying transcription factor footprints.  ...  factor footprints.  ...  Affiliations National Key Laboratory of Crop Genetic Improvement, Huazhong  ... 
doi:10.1101/2020.10.22.351478 fatcat:lsqrkx4j4jhcvapl66cntbktpq
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