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MATCHTM: a tool for searching transcription factor binding sites in DNA sequences
2003
Nucleic Acids Research
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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
2021
Biology
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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
2006
BMC Bioinformatics
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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
2010
PLoS ONE
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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
2009
Nucleic Acids Research
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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
2006
Bioinformatics
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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
2019
BMC Bioinformatics
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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
2016
PLoS ONE
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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
2013
Glycobiology
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) , 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
2009
Clinical Chemistry
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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
2015
BMC Bioinformatics
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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
2007
BMC Developmental Biology
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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
2005
Theoretical Biology and Medical Modelling
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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
2008
Genome Biology
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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
2010
Journal of Molecular Medicine
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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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