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TRANSFAC: an integrated system for gene expression regulation

E. Wingender
2000 Nucleic Acids Research  
Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs and cell types, have been extended and are increasingly integrated with the TRANSFAC data sources.  ...  Moreover, TRANSFAC has been extended by two new modules: PathoDB provides data on pathologically relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features  ...  Finally, we express our gratitude to Mrs A. Bischoff for the technical help in nearly all the abovementioned fields. Parts of this work were supported by the  ... 
doi:10.1093/nar/28.1.316 pmid:10592259 pmcid:PMC102445 fatcat:c4um2wfgdzhylowqzpagcwt2cq

The TRANSFAC System on Gene Regulation
発現制御に関するデータベースシステム TRANSFAC

Edgar Wingender
2000 Trends in glycoscience and glycotechnology  
The TRANSFAC system comprises a number of originally independent databases on gene regulation.  ...  A short description of the individual database modules and the associated programs as well as an outlook to future perspectives is given.  ...  CYTOMER serves as the basis to derive an "ontology" for gene expression locations and stages.  ... 
doi:10.4052/tigg.12.255 fatcat:t343pbenhfa33c2bqlocadhipy

The TRANSFAC system on gene expression regulation

E. Wingender
2001 Nucleic Acids Research  
(TRANSPATH) and gene expression sources (CYTOMER).  ...  Altogether, these distinct database modules constitute the TRANSFAC system.  ...  Finally, we express our gratitude to Mrs A. Bischoff for the technical help in nearly all of the above-mentioned fields.  ... 
doi:10.1093/nar/29.1.281 pmid:11125113 pmcid:PMC29801 fatcat:u3d65o47wbbfpggwzo6pfrdjoa

TRANSFAC(R): transcriptional regulation, from patterns to profiles

V. Matys
2003 Nucleic Acids Research  
For yeast an additional release including the latest data was made available separately as TRANSFAC 1 Saccharomyces Module (TSM) at http://transfac. gbf.de.  ...  The TRANSFAC 1 database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both  ...  ACKNOWLEDGEMENTS We would like to thank all present and former members of BIOBASE GmbH and the AG Bioinformatics at the German Research Centre for Biotechnology (GBF) for contributing to this work in various  ... 
doi:10.1093/nar/gkg108 pmid:12520026 pmcid:PMC165555 fatcat:3hjrkzoaxnhafl2mfo2qhtv52a

TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation

E. Wingender, A. E. Kel, O. V. Kel, H. Karas, T. Heinemeyer, P. Dietze, R. Knuppel, A. G. Romaschenko, N. A. Kolchanov
1997 Nucleic Acids Research  
Three databases that provide data on transcriptional regulation are described. TRANSFAC is a database on transcription factors and their DNA binding sites.  ...  TRRD (Transcription Regulatory Region Database) collects information about complete regulatory regions, their regulation properties and architecture.  ...  Shomer (EBI, Hinxton) for supporting the mutual database cross-referencing.  ... 
doi:10.1093/nar/25.1.265 pmid:9016550 pmcid:PMC146363 fatcat:3lpoh42y2ffvvplppopi2jgci4

Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms

T. Heinemeyer, X. Chen, H. Karas, A. E. Kel, O. V. Kel, I. Liebich, T. Meinhardt, I. Reuter, F. Schacherer, E. Wingender
1999 Nucleic Acids Research  
TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles.  ...  Among them, modules which provide data about signal transduction pathways (TRANSPATH) or about cell types/organs/developmental stages (CYTOMER) are available as well as an updated version of the previously  ...  Hermjakob (EBI, Hinxton, UK) for his support in establishing TRANSFAC-links to the EMBL data library and to the SwissProt database, and to M.  ... 
doi:10.1093/nar/27.1.318 pmid:9847216 pmcid:PMC148171 fatcat:fjpblo3scrcv7fhpt75ttmc7vy

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

E. Wingender
2008 Briefings in Bioinformatics  
Since its beginning as a data collection more than 20 years ago, the TRANSFAC project underwent an evolution to become the basis for a complex platform for the description and analysis of gene regulatory  ...  In the following, I describe what the original concepts were, what their present status is and how they may be expected to contribute to future system biology approaches.  ...  regulation of gene expression plays an important role, for instance, in tumorigenesis [17, 18] .  ... 
doi:10.1093/bib/bbn016 pmid:18436575 fatcat:5umimjlklvfx3nuuchv5gpkuoa

Bioinformatic detection of E47, E2F1 and SREBP1 transcription factors as potential regulators of genes associated to acquisition of endometrial receptivity

Alejandro Tapia, Cristian Vilos, Juan Marín, Horacio B Croxatto, Luigi Devoto
2011 Reproductive Biology and Endocrinology  
Its main function is to provide an adequate substrate for embryo implantation.  ...  The discovery of possible new transcription factors orchestrating the CERTL opens new alternatives for understanding gene expression regulation in uterine function.  ...  Cecilia Johnson (IDIMI, Universidad de Chile, Santiago, Chile) for their helpful comments and critical review of the article.  ... 
doi:10.1186/1477-7827-9-14 pmid:21272326 pmcid:PMC3040129 fatcat:mxa2l74exbcepplxvgk2smqbby

Identifying transcriptional regulatory sites in the human genome using an integrated system

H.-D. Huang
2004 Nucleic Acids Research  
This work develops an integrated system which, after a set of genes are inputted, is able to predict transcriptional regulatory sites and to detect the cooccurrence of these regulatory sites.  ...  By comparing these sites with previously published results, the proposed system is able to help biologists identify possible candidates for the regulatory sites from groups of co-regulated genes.  ...  They also thank Professor Cheng-Yan Kao for his valuable suggestions and comments.  ... 
doi:10.1093/nar/gkh345 pmid:15051813 pmcid:PMC390354 fatcat:lr6mujnvjvhhnmpodlxhstm7zm

Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection

Elena Zaslavsky, German Nudelman, Susanna Marquez, Uri Hershberg, Boris M Hartmann, Juilee Thakar, Stuart C Sealfon, Steven H Kleinstein
2013 BMC Bioinformatics  
To provide a mechanistic explanation for the timing of gene expression changes over the first 12 hours post-infection, we developed a statistically rigorous enrichment approach integrating genome-wide  ...  Results: Genome-wide gene expression patterns were measured in human monocyte-derived dendritic cells (DCs) infected in vitro with seasonal H1N1 influenza A/New Caledonia/20/1999.  ...  Duke for generating the transcription factor target data.  ... 
doi:10.1186/1471-2105-14-s6-s1 pmid:23734902 pmcid:PMC3633009 fatcat:lzvynnkxobcfbm6jdmdcjdvxxe

Computational framework for the prediction of transcription factor binding sites by multiple data integration

Alberto Ambesi-Impiombato, Mukesh Bansal, Pietro Liò, Diego di Bernardo
2006 BMC Neuroscience  
We show the advantages of integrating information based on evolutionary conservation and gene expression, when tackling the problem of binding site prediction.  ...  However, biological mechanisms underlying the regulation of gene expression are not completely understood, and predictions via bioinformatics tools are typically poorly specific.  ...  Acknowledgements This article has been published as part of BMC Neuroscience Volume 7, Supplement 1, 2006: Problems and tools in the systems biology of the neuronal cell.  ... 
doi:10.1186/1471-2202-7-s1-s8 pmid:17118162 pmcid:PMC1775048 fatcat:p26lss5y2jcc7nopouxs7etqjq

Transcription Regulatory Regions Database (TRRD): its status in 1999

N. A. Kolchanov, E. A. Ananko, O. A. Podkolodnaya, E. V. Ignatieva, I. L. Stepanenko, O. V. Kel-Margoulis, A. E. Kel, T. I. Merkulova, T. N. Goryachkovskaya, T. V. Busygina, F. A. Kolpakov, N. L. Podkolodny (+2 others)
1999 Nucleic Acids Research  
contain, i.e., transcription factor binding sites, promoters, enhancers, silencers, etc., and expression patterns of the genes.  ...  The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes, the regulatory elements they  ...  The work is supported by the Russian Foundation for Basic Research (grants Nos. 96-04-50006, 97-04-49740, 98-04-49479, 98-07-91078), Integration Program of Siberian Branch of Russian Academy of Sciences  ... 
doi:10.1093/nar/27.1.303 pmid:9847210 pmcid:PMC148165 fatcat:u2pzqpx375eqfmko5qvsh4b4qu

Analysis of miRNA, mRNA, and TF interactions through network-based methods

Pietro H Guzzi, Maria Teresa Di Martino, Pierosandro Tagliaferri, Pierfrancesco Tassone, Mario Cannataro
2015 EURASIP Journal on Bioinformatics and Systems Biology  
The need for an introductive survey from a computer science point of view consequently arises. This survey starts by discussing general concepts related to production of data.  ...  The comprehensive analysis is made possible only by the integration and the analysis of these data sources.  ...  Acknowledgements This work has been supported by the Italian Association for Cancer Research (AIRC), PI: PT. "Special Program Molecular Clinical Oncology -5 per mille" n.  ... 
doi:10.1186/s13637-015-0023-8 pmid:28194173 pmcid:PMC5270379 fatcat:ghnojnoitbes3gmvlbmwxqgspe

MADNet: microarray database network web server

I. Segota, N. Bartonicek, K. Vlahovicek
2008 Nucleic Acids Research  
(TRANSFAC!)  ...  These data are integrated with information stored in various biological databases such as NCBI nucleotide and protein databases, metabolic and signalling pathway databases (KEGG), transcription regulation  ...  Funding to pay the Open Access publication charges for this article was provided by EMBO. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkn289 pmid:18480121 pmcid:PMC2447778 fatcat:tjbkdgdolzfubhkyyczbopjbxa

Antiviral Response Dictated by Choreographed Cascade of Transcription Factors

E. Zaslavsky, U. Hershberg, J. Seto, A. M. Pham, S. Marquez, J. L. Duke, J. G. Wetmur, B. R. tenOever, S. C. Sealfon, S. H. Kleinstein
2010 Journal of Immunology  
I Novel TFs predicted by the network analysis Gene symbol TRANSFAC Matrix TRANSFAC Motif First Expressed (h) Table II .  ...  Only vertebrate TRANSFAC matrices that could be linked to a human (HGNC) gene symbol (30) , either directly or through an alias listed in National Center for Biotechnology Information gene, were included  ... 
doi:10.4049/jimmunol.0903453 pmid:20164420 pmcid:PMC2856074 fatcat:oac6hawazfepfb5knl6dxlx26i
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