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footprintDB: a database of transcription factors with annotated cis elements and binding interfaces

Alvaro Sebastian, Bruno Contreras-Moreira
2013 Computer applications in the biosciences : CABIOS  
Results: FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites (DBSs), and systematically annotates the binding interfaces of the corresponding transcription  ...  A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while  ...  ACKNOWLEDGEMENTS We thank our colleagues from the STREG project (L.Bülow, R.Hehl, G.Huep, B.Weisshaar, C.Dubos, L.Lepiniec and A.Koller) for their feedback and support while developing this resource.  ... 
doi:10.1093/bioinformatics/btt663 pmid:24234003 fatcat:fmfks636yrb4nm6htdx3r7gfgu

FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces [chapter]

Bruno Contreras-Moreira, Alvaro Sebastian
2016 Msphere  
FootprintDB is a database and search engine that compiles regulatory sequences from open access libraries of curated DNA cis-elements and motifs, and their associated transcription factors (TFs).  ...  It systematically annotates the binding interfaces of the TFs by exploiting protein-DNA complexes deposited in the Protein Data Bank.  ...  Serra and J. van Helden for past and current collaborations.  ... 
doi:10.1007/978-1-4939-6396-6_17 pmid:27557773 fatcat:wnjluag6mfazflewblzgmvosqi

Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes

Christian Dubos, Zsolt Kelemen, Alvaro Sebastian, Lorenz Bülow, Gunnar Huep, Wenjia Xu, Damaris Grain, Fabien Salsac, Cecile Brousse, Loïc Lepiniec, Bernd Weisshaar, Bruno Contreras-Moreira (+1 others)
2014 BMC Genomics  
In contrast, the identification of the transcription factors (TFs) interacting with these cis-sequences is much more elaborate.  ...  All motifs were subjected to a footprintDB analysis to predict interacting DNA binding domains from plant TF families.  ...  The authors would like to acknowledge the support of Jasmin Huebner and Nina Schmidt in the generation and analysis of transgenic A. thaliana. We also acknowledge F. Turck (MPI, Köln) and V.  ... 
doi:10.1186/1471-2164-15-317 pmid:24773781 pmcid:PMC4234446 fatcat:t3ef5p2t4vb5vc5nnjod2nwggi

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

Sushil Tripathi, Steven Vercruysse, Konika Chawla, Karen R. Christie, Judith A. Blake, Rachael P. Huntley, Sandra Orchard, Henning Hermjakob, Liv Thommesen, Astrid Lægreid, Martin Kuiper
2016 Database: The Journal of Biological Databases and Curation  
We demonstrate this with a project in which we mobilize biological domain experts who curate large amounts of DNA binding transcription factors, and show that they, although new to the field of curation  ...  A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives.  ...  Acknowledgements We thank Tony Sawford for assistance and guidance in submitting DbTF-annotations to the GO database, and Marine Dumousseau and Maximilian Koch for assistance and guidance in submitting  ... 
doi:10.1093/database/baw088 pmid:27270715 pmcid:PMC4911790 fatcat:bgvk2mjfxrcinmhz5jykd3cotq

SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes

Teshome Dagne Mulugeta, Torfinn Nome, Thu-Hien To, Manu Kumar Gundappa, Daniel J. Macqueen, Dag Inge Våge, Simen Rød Sandve, Torgeir R. Hvidsten
2019 BMC Genomics  
We present SalMotifDB, a database and associated web and R interface for the analysis of transcription factors (TFs) and their cis-regulatory binding sites in five salmonid genomes.  ...  SalMotifDB is an effective tool for analyzing transcription factors, their binding sites and the resulting gene regulatory networks in salmonid species, and will be an important tool for gaining a better  ...  Microfluidics-based Ligand Enrichment followed by Sequencing; SP: Specificity Protein; SREBP: Sterol Regulatory Element Binding Protein; TF: Transcription Factor; TRANSFAC: TRANScription FACtor database  ... 
doi:10.1186/s12864-019-6051-0 pmid:31477007 pmcid:PMC6720087 fatcat:kcljic44nvdbpa6jzjuyhbseii

Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model [article]

Najla Ksouri, Jaime Abraham Castro-Mondragón, Francesc Montardit-Tardà, Jacques van Helden, Bruno Contreras-Moreira, Yolanda Gogorcena
2020 bioRxiv   pre-print
These predictions rely on the construction of a co-expression network to generate modules with similar expression trends and assess the effect of increasing upstream region length on the sensitivity of  ...  The spatial distribution of TF binding sites revealed an unbalanced distribution where motifs tend to lie around the transcriptional start site region.  ...  TF match: Transcription factor family of the best match in footprintDB.523 Ncor: normalized Pearson correlation varying between 0 and 1. Ncor ≥ 0.4 indicates 524 high confidence annotations.  ... 
doi:10.1101/2020.02.28.970137 fatcat:4fxibs2645dyxb32hwenw7w3my

Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example

Najla Ksouri, Jaime A Castro-Mondragón, Francesc Montardit-Tarda, Jacques van Helden, Bruno Contreras-Moreira, Yolanda Gogorcena
2021 Plant Physiology  
Overall, 18 out of 45 co-expressed modules were enriched in motifs typical of well-known transcription factor (TF) families (bHLH, bZip, BZR, CAMTA, DOF, E2FE, AP2-ERF, Myb-like, NAC, TCP, and WRKY) and  ...  The method was also verified on maize (Zea mays), a species with a large genome.  ...  Funding This work was partly funded by the Spanish Ministry of Economy and Competitiveness grants AGL2014-52063R, AGL2017-83358-R (MCIU/AEI/FEDER/UE); and the Government of Aragón with grants A44, A08_  ... 
doi:10.1093/plphys/kiaa091 pmid:33744946 pmcid:PMC8133646 fatcat:7zhwcc7mbvgjnf6c6zc3fuvogu

ApicoTFdb: The comprehensive web repository of apicomplexan transcription factors and regulators [article]

Rahila Sardar, Abhinav Kaushik, Rajan Pandey, Asif Mohmmed, Shakir Ali, Dinesh Gupta
2019 bioRxiv   pre-print
, with only a limited number of non-AP2 family TFs and TAFs.  ...  We have performed systematic bioinformatics aided prediction of TFs and TAFs in apicomplexan genomes, and developed ApicoTFdb database which consists of experimentally validated as well as computationally  ...  Contreras-Moreira B, Sebastian A: FootprintDB: Analysis of Plant Cis-Regulatory Elements, 357 Transcription Factors, and Binding Interfaces.  ... 
doi:10.1101/530006 fatcat:fkxae7lwirdedbyxktgfyrexti

RSAT Variation-tools: an accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding

Walter Santana-Garcia, Maria Rocha-Acevedo, Lucia Ramirez-Navarro, Yvon Mbouamboua, Denis Thieffry, Morgane Thomas-Chollier, Bruno Contreras-Moreira, Jacques van Helden, Alejandra Medina-Rivera
2019 Computational and Structural Biotechnology Journal  
Gene regulatory regions contain short and degenerated DNA binding sites recognized by transcription factors (TFBS).  ...  The tools are included within the well-maintained suite Regulatory Sequence Analysis Tools (RSAT, http://rsat.eu), and accessible through a web interface that currently enables analysis of five metazoa  ...  We acknowledge Salvatore Spicuglia for useful comments during the development of the tools. We thank Lambert Moyon and Swann Floc'hlay for providing feedback on the use of Variation-tools.  ... 
doi:10.1016/j.csbj.2019.09.009 pmid:31871587 pmcid:PMC6906655 fatcat:z7k3s2mu5nb6zilrzdon7nvszm

RSAT 2018: regulatory sequence analysis tools 20th anniversary

Nga Thi Thuy Nguyen, Bruno Contreras-Moreira, Jaime A Castro-Mondragon, Walter Santana-Garcia, Raul Ossio, Carla Daniela Robles-Espinoza, Mathieu Bahin, Samuel Collombet, Pierre Vincens, Denis Thieffry, Jacques van Helden, Alejandra Medina-Rivera (+1 others)
2018 Nucleic Acids Research  
RSAT (Regulatory Sequence Analysis Tools) is a suite of modular tools for the detection and the analysis of cis-regulatory elements in genome sequences.  ...  Three use cases illustrate the integration of new and refactored tools to the suite. This Anniversary update gives a 20year perspective on the software suite.  ...  ACKNOWLEDGEMENTS We are particularly thankful to the colleagues who help us installing and maintaining RSAT servers: Victor del Moral Chavez, Romualdo Zayas-Lagunas, Alfredo José Hernández Alvarez (Centro  ... 
doi:10.1093/nar/gky317 pmid:29722874 pmcid:PMC6030903 fatcat:hau274l2trgfhhtpxtwsqftyna

RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes [chapter]

Jaime A. Castro-Mondragon, Claire Rioualen, Bruno Contreras-Moreira, Jacques van Helden
2016 Msphere  
In this protocol we explain how to run ab initio motif discovery in order to gather putative transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP-seq experiments.  ...  We provide a concise description of the successive steps to discover motifs, cluster the motifs returned by different motif discovery algorithms, and compare them with reference motif databases.  ...  Add your own motif database allows you to upload a custom database of transcription factor binding motifs in a TRANSFAC-formatted file. 10 If there is a known motif for the immunoprecipitated factor,  ... 
doi:10.1007/978-1-4939-6396-6_19 pmid:27557775 fatcat:uf4jvjkdw5ed5h4jy6bhwui3si

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections [article]

Jaime Castro-Mondragon, Sebastien Jaeger, Denis Thieffry, Morgane Thomas-Chollier, Jacques van Helden
2016 bioRxiv   pre-print
Transcription Factor (TF) databases contain multitudes of motifs from various sources, from which non-redundant collections are derived by manual curation.  ...  The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs.  ...  We are also thankful to the JASPAR team for check and validate the clustering of JASPAR motif collections.  ... 
doi:10.1101/065565 fatcat:jgrxzdfos5a5vhhig2pqghiqje

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

Jaime Abraham Castro-Mondragon, Sébastien Jaeger, Denis Thieffry, Morgane Thomas-Chollier, Jacques van Helden
2017 Nucleic Acids Research  
Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation.  ...  The advent of highthroughput methods stimulated the production of novel collections with increasing numbers of motifs.  ...  We are also thankful to the JASPAR team for checking and validating the clustering of JASPAR motif collections. FUNDING  ... 
doi:10.1093/nar/gkx314 pmid:28591841 pmcid:PMC5737723 fatcat:pzkqst4x4rfsva2scmnib75omq

RSAT 2015: Regulatory Sequence Analysis Tools

Alejandra Medina-Rivera, Matthieu Defrance, Olivier Sand, Carl Herrmann, Jaime A. Castro-Mondragon, Jeremy Delerce, Sébastien Jaeger, Christophe Blanchet, Pierre Vincens, Christophe Caron, Daniel M. Staines, Bruno Contreras-Moreira (+6 others)
2015 Nucleic Acids Research  
Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii  ...  RSAT (Regulatory Sequence Analysis Tools ) is a modular software suite for the analysis of cisregulatory elements in genome sequences.  ...  ACKNOWLEDGEMENTS We are particularly thankful to the colleagues who help us in installing and maintaining RSAT servers: Victor del Moral Chavez, Romualdo Zayas-Lagunas, Alfredo José  ... 
doi:10.1093/nar/gkv362 pmid:25904632 pmcid:PMC4489296 fatcat:jzbr4up77jcghnkc3hzsbwdrjq

Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace

Carlos P. Cantalapiedra, María J. García-Pereira, María P. Gracia, Ernesto Igartua, Ana M. Casas, Bruno Contreras-Moreira
2017 Frontiers in Plant Science  
Overall, 11 transcription factors were identified, and one of them matched cis-regulatory motifs discovered upstream of co-expressed genes involved in those responses.  ...  transcripts.  ...  However, analyses of cis-regulatory elements of transcription factors (TFs) and of promoters of genes involved in a given response have been rare in barley, likely due to the absence of adequate genomics  ... 
doi:10.3389/fpls.2017.00647 pmid:28507554 pmcid:PMC5410667 fatcat:cj4vg5lnv5e5jfnaxgqnl2xu7y
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