Transcription Factor Binding Site Prediction

Using TF matrices to predict TF binding sites (TFBS) in regions of interest. I have seen TRANSFAC and JASPAR mentioned in relation to TF matrices. I have found some text files in the JASPAR database that seem like what I need and I will probably use these. Would anybody know if these are any different

The hemochromatosis protein HFE competes with transferrin for binding to the transferrin receptor

View ScienceDirect over a secure connection:switch to HTTPS The hemochromatosis protein HFE competes with transferrin for binding to the transferrin receptor HFE is a class I major histocompatibility complex (MHC)-related protein that is mutated in patients with the iron overload disease hereditary hemochromatosis. HFE binds to transferrin receptor (TfR), the receptor used by cells to


TF_binding_site_variant (CURRENT_SVN) A sequence variant located within a transcription factor binding site. Jannovar:tf_binding_site_variant, TF binding site variant, VEP:TF_binding_site_variant regulatory_region_variant (SO:0001566) In the image below graph nodes link to the appropriate terms. Clicking the image background will toggle the image between large and small formats.


Software for motif discovery and next-sequencing analysis Motif Databases included in HOMERHomer includes several motif databases that are used to help annotate results and conduct searches for known motifs. HOMER contains a custom motif database based on independent analysis of mostly ChIP-Seq data sets which is heavily utilized in the software. Below is a description


watchedObject.symbol (RGD ID:watchedObject.rgdId) watchedTerm.term (watchedTerm.accId) Select categories you would like to watch. Updates to this gene will be send to username -1 ng-click=toggleGeneWatchSelection(geneWatchAttr) CancelStop WatchingSaveAnalyzeGeneStrainQTLListFunctional Annotation unavailableDamaging Variants unavailbleDamaging Variants RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.

AGRIS Binding Sites List

Guiltinan MJ, Marcotte WR Jr, Quatrano RS. A plant leucine zipper protein that recognizes an abscisic acid response element Choi H, Hong J, Ha J, Kang J, Kim SY ABFs, a family of ABA-responsive element binding factors Shinozaki K., Yamaguchi-Shinozaki K. Molecular responses to dehydration and low temperature Curr. Opin. Plant Biol. (2000) 3:217-223 Hartmann


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The regulatory role of decoy transcription factor binding sites

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Transcription FactorDNA Binding Motifs in

The DNA binding specificity of transcription factors (TFs) is typically represented in the form of a position weight matrix (PWM), also known as a DNA motif. A PWM is a matrix that specifies, for each position in the DNA binding site of a TF, the weight or contribution of each possible nucleotide. DNA motifs can

Core seminar

Users who wish to get an introduction to the central concepts, strategies, and analysis software offered by Genomatix for transcription factor binding site and promoter analysis, and to learn how to apply them most efficiently. Lectures on theoretical background alternate with practical hands-on examples under the guidance of an instructor. 2 days, approx. 6-7 hrs.

The binding site for the liver-specific transcription factor Tf-LF1 and the TATA box of the

We have studied the liver-specific transcriptional activity of the human transferrin gene promoter. Results of competition experiments, site-directed mutagenesis, and 5 deletion analysis have demonstrated that a TATA box and a binding site for the liver-specific protein Tf-LF1 are the only elements needed to direct hepatic-specific transcription in vitro. Thus, Tf-LF1 behaves as other previously

MATCH — a tool for searching transcription factor binding sites in DNA sequences

OBRC: Online Bioinformatics Resources Collection MATCH — a tool for searching transcription factor binding sites in DNA sequences Search potential binding sites for transcription factors (TF binding sites) nucleotide sequences. MatchTM is a weight matrix-based tool for searching putative transcription factor binding sites in DNA sequences. MatchTM is closely interconnected and distributed together with the


Ask your biological question, and let the search engine handle the rest. Bookmark tools and put favorites into folders to find them easily. A user-friendly web resource for genome-scale exploration of gene regulation in Arabidopsis thaliana Incorporates a variety of genome-wide data types relevant to gene regulation. CressInt is a user-friendly, freely accessible web server