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MATCHTM: a tool for searching transcription factor binding sites in DNA sequences

A.E. Kel
2003 Nucleic Acids Research  
Match TM is a weight matrix-based tool for searching putative transcription factor binding sites in DNA sequences.  ...  In particular, Match TM uses the matrix library collected in TRANSFAC 1 and therefore provides the possibility to search for a great variety of different transcription factor binding sites.  ...  Part of this work was supported by Siberian Branch of Russian Academy of Sciences and by a grant of the European Commission (BIO4-95-0226).  ... 
doi:10.1093/nar/gkg585 pmid:12824369 pmcid:PMC169193 fatcat:x5wbyuom3vcmdifmgkfcfwjovq

agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal Species

Selina Klees, Felix Heinrich, Armin Otto Schmitt, Mehmet Gültas
2021 Biology  
Transcription factors (TFs) govern transcriptional gene regulation by specifically binding to short DNA motifs, known as transcription factor binding sites (TFBSs), in regulatory regions, such as promoters  ...  Altogether, we implemented the first systematic analysis of SNPs in promoter regions and their impact on the binding affinity of TFs for livestock and made it usable via a web interface.  ...  TFs regulate the transcription as a response to specific environmental conditions by binding to short degenerate sequence motifs known as transcription factor binding sites (TFBSs) in promoter regions  ... 
doi:10.3390/biology10080790 fatcat:bbioybeex5bh7mpavxtu6ju34a

Beyond microarrays: Finding key transcription factors controlling signal transduction pathways

Alexdander Kel, Nico Voss, Ruy Jauregui, Olga Kel-Margoulis, Edgar Wingender
2006 BMC Bioinformatics  
Transcription factors constitute a class of the regulatory molecules that typically require posttranscriptional modifications or ligand binding in order to exert their function.  ...  We demonstrate that promoters of genes encoding components of many known signal transduction pathways are enriched by binding sites of those transcription factors that are endpoints of the considered pathways  ...  We have developed two computational tools: F-Match™ for revealing over-and underrepresented sites of promoters and ArrayAnalyzer™ for identification of key nodes in signal transduction networks.  ... 
doi:10.1186/1471-2105-7-s2-s13 pmid:17118134 pmcid:PMC1683568 fatcat:zdusg6vf2jhqzcknrr3cletlwy

A Bayesian Search for Transcriptional Motifs

Andrew K. Miller, Cristin G. Print, Poul M. F. Nielsen, Edmund J. Crampin, Diego Di Bernardo
2010 PLoS ONE  
Identifying transcription factor (TF) binding sites (TFBSs) is an important step towards understanding transcriptional regulation.  ...  We tested SBaSeTraM against a MATCHTM implementation by searching all probes used in an experimental Saccharomyces cerevisiae TF binding dataset, and comparing our predictions to the data.  ...  Acknowledgments The authors would like to thank the two anonymous reviewers for providing helpful feedback on this manuscript. Author Contributions  ... 
doi:10.1371/journal.pone.0013897 pmid:21124986 pmcid:PMC2987817 fatcat:fk3fhio765ckjfxfbdzrme5v2u

miRGen 2.0: a database of microRNA genomic information and regulation

Panagiotis Alexiou, Thanasis Vergoulis, Martin Gleditzsch, George Prekas, Theodore Dalamagas, Molly Megraw, Ivo Grosse, Timos Sellis, Artemis G. Hatzigeorgiou
2009 Nucleic Acids Research  
microRNA coding transcripts and their regulation by transcription factors, including a unique compilation of both predicted and experimentally supported data.  ...  MicroRNAs are produced from longer transcripts which can code for more than one mature miRNAs. miRGen 2.0 is a database that aims to provide comprehensive information about the position of human and mouse  ...  Searching for a TF of interest (Figure 3b ) returns all miRNA coding genes for which at least one binding site for this TF is found.  ... 
doi:10.1093/nar/gkp888 pmid:19850714 pmcid:PMC2808909 fatcat:kes3cztwyrdypawuklnrbwuz4y

Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations

A. Kel, T. Konovalova, T. Waleev, E. Cheremushkin, O. Kel-Margoulis, E. Wingender
2006 Bioinformatics  
Results: Here we present a new approach for defining promoter models based on the composition of transcription factor binding sites and their pairs.  ...  Such regulation is provided by precisely organized binding of a multiplicity of special proteins (transcription factors) to their target sites (cis-elements) in regulatory regions of genes.  ...  Research (BMBF) together with BioRegioN GmbH "BioProfil", grant no. 0313092; "Intergenomics" Project, Grant No. 031U110C/031U210C; by European Commission under FP6-"Life sciences, genomics and biotechnology for  ... 
doi:10.1093/bioinformatics/btl041 pmid:16473870 fatcat:ae2lboreezgtpld2mxauuxtedy

Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

Alexander Kel, Ulyana Boyarskikh, Philip Stegmaier, Leonid S. Leskov, Andrey V. Sokolov, Ivan Yevshin, Nikita Mandrik, Daria Stelmashenko, Jeannette Koschmann, Olga Kel-Margoulis, Mathias Krull, Anna Martínez-Cardús (+5 others)
2019 BMC Bioinformatics  
Methods: We have developed a method for finding potential causal relationships between epigenetic changes (DNA methylations) in gene regulatory regions that affect transcription factor binding sites (TFBS  ...  We call this method "Walking pathways", since it searches for potential rewiring mechanisms in cancer pathways due to dynamic changes in the DNA methylation status of important gene regulatory regions  ...  previously in [6, 7] ).  ... 
doi:10.1186/s12859-019-2687-7 fatcat:6hei6dbog5ewznngqax62wmphy

Gene Regulatory Network Inference of Immunoresponsive Gene 1 (IRG1) Identifies Interferon Regulatory Factor 1 (IRF1) as Its Transcriptional Regulator in Mammalian Macrophages

Aravind Tallam, Thaneer M. Perumal, Paul M. Antony, Christian Jäger, Joëlle V. Fritz, Laurent Vallar, Rudi Balling, Antonio del Sol, Alessandro Michelucci, Geraldo A Passos
2016 PLoS ONE  
Furthermore, using literature information and transcription factor prediction models, we re-constructed raw gene regulatory networks (GRNs) for IRG1 in mouse and human macrophages.  ...  A volume of 150μL/well of M-PER complete reagent was added IRF1 Is a Transcriptional Regulator of IRG1  ...  Lasse Sinkkonen for helping with human RNA samples for microarrays experiments. We are grateful to François Bernardin and Dr.  ... 
doi:10.1371/journal.pone.0149050 pmid:26872335 pmcid:PMC4752512 fatcat:63wyvbowm5antnkxaix66m7ydq

Copy-number variation of functional galectin genes: Studying animal galectin-7 (p53-induced gene 1 in man) and tandem-repeat-type galectins-4 and -9

Herbert Kaltner, Anne-Sarah Raschta, Joachim C Manning, Hans-Joachim Gabius
2013 Glycobiology  
) , also led to identification of sequence motifs that satisfy the criteria of a binding site for transcription factors.  ...  Both sequences were systematically aligned to known motifs for binding transcription factors.  ... 
doi:10.1093/glycob/cwt052 pmid:23840039 fatcat:5pvcylm4frcxnl7h66d23y6vqu

Management of Gene Promoter Mutations in Molecular Diagnostics

K. M. K. de Vooght, R. van Wijk, W. W. van Solinge
2009 Clinical Chemistry  
Characterization of a promoter sequence variation includes a comprehensive study of the literature and databases of human mutations and transcription factors.  ...  BACKGROUND: Although promoter mutations are known to cause functionally important consequences for gene expression, promoter analysis is not a regular part of DNA diagnostics.  ...  ), TFs TF-binding site prediction TESS (Transcription Element Search System) http://www.cbil.upenn.edu/cgi-bin/tess/tess TF-binding site prediction Match™ http://www.gene-regulation.com/cgi-bin  ... 
doi:10.1373/clinchem.2008.120931 pmid:19246615 fatcat:4kk6msrdxref5drskstmug5cb4

PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

Cornelia Meckbach, Rebecca Tacke, Xu Hua, Stephan Waack, Edgar Wingender, Mehmet Gültas
2015 BMC Bioinformatics  
collaborating transcription factors based on the idiosyncrasy of their binding site distributions on the genome.  ...  In this study, we present a new method based on pointwise mutual information, PC-TraFF, which considers the genome as a document, the sequences as sentences, and TF binding sites (TFBSs) as words to identify  ...  Acknowledgments We thank our colleagues Martin Haubrock, Darius Wlochowitz, and Sebastian Zeidler for their helpful advice and insights at early stages of this project and for comments on the results.  ... 
doi:10.1186/s12859-015-0827-2 pmid:26627005 pmcid:PMC4667426 fatcat:pcq3twh7qjde3n7y734kaxb44q

Hand is a direct target of the forkhead transcription factor Biniou during Drosophila visceral mesoderm differentiation

Dmitry Popichenko, Julia Sellin, Marek Bartkuhn, Achim Paululat
2007 BMC Developmental Biology  
Combining functional dissection experiments in vivo and protein/DNA binding studies we identified hand as a direct target of Biniou in the circular visceral muscles.  ...  We found that hand expression in the circular visceral mesoderm is abolished in embryos mutant for the FoxF domain containing transcription factor Biniou.  ...  We thank Martina Biedermann and Mechthild Krabusch for excellent technical assistance. This work was supported by grants from the DFG to A.P.  ... 
doi:10.1186/1471-213x-7-49 pmid:17511863 pmcid:PMC1891290 fatcat:esorvwi53jcfrn72empciv7pbu

Construction of predictive promoter models on the example of antibacterial response of human epithelial cells

Ekaterina Shelest, Edgar Wingender
2005 Theoretical Biology and Medical Modelling  
The model construction is based on the consideration of pair-wise combinations of transcription factor binding sites (TFBS).  ...  Binding of a bacteria to a eukaryotic cell triggers a complex network of interactions in and between both cells.  ...  Acknowledgements The authors would like to thank Ingmar Reuter, Ellen Goessling and Dmitri Tchekmenev for technical help and Alexander Kel for helpful discussions.  ... 
doi:10.1186/1742-4682-2-2 pmid:15647113 pmcid:PMC546226 fatcat:ssqwc4bsnnhshioqgfl53q6jrq

Genome wide prediction of HNF4α functional binding sites by the use of local and global sequence context

Alexander E Kel, Monika Niehof, Volker Matys, Rüdiger Zemlin, Jürgen Borlak
2008 Genome Biology  
We report an application of machine learning algorithms that enables prediction of the functional context of transcription factor binding sites in the human genome.  ...  The technique can be applied to any transcription factor.  ...  Background Regulation of gene expression is accomplished through binding of transcription factors (TFs) to distinct regions of DNA (TF binding sites (TFBSs)), and, after anchoring at these sites, transmission  ... 
doi:10.1186/gb-2008-9-2-r36 pmid:18291023 pmcid:PMC2374721 fatcat:2xp4hp36pbbkfl7qma47ihwvpe

Methylation matters: binding of Ets-1 to the demethylated Foxp3 gene contributes to the stabilization of Foxp3 expression in regulatory T cells

Julia K. Polansky, Lisa Schreiber, Christoph Thelemann, Leif Ludwig, Melanie Krüger, Ria Baumgrass, Sascha Cording, Stefan Floess, Alf Hamann, Jochen Huehn
2010 Journal of Molecular Medicine  
The forkhead-box protein P3 (Foxp3) is a key transcription factor for the development and suppressive activity of regulatory T cells (Tregs), a T cell subset critically involved in the maintenance of self-tolerance  ...  for essential transcription factors, such as CREB/ATF and NF-κB, which have previously been shown to bind to this element.  ...  In addition, we are grateful to all members of the Huehn and Hamann labs for fruitful discussions. This work has been supported by the German Research Foundation (DFG, SFB738-C7 and SFB650-TP1).  ... 
doi:10.1007/s00109-010-0642-1 pmid:20574810 pmcid:PMC2943068 fatcat:mgaic6vlwrainnbbd6dij3ubia
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