:: DESCRIPTION
MotifAdjuster is a tool for computational reassessment of transcription factor binding site annotations
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2009;10(5):R46. doi: 10.1186/gb-2009-10-5-r46. Epub 2009 May 1.
MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations.
Keilwagen J1, Baumbach J, Kohl TA, Grosse I.
:: DESCRIPTION
DACO (domain-aware cohesiveness optimization) is a novel algorithm that combines protein-protein interaction networks and domain-domain interaction networks with the cluster-quality metric cohesiveness.
::DEVELOPER
Chair of Computational Biology at the Saarland University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Sep 1;30(17):i415-i421. doi: 10.1093/bioinformatics/btu448.
Identifying transcription factor complexes and their roles.
Will T, Helms V.
:: DESCRIPTION
TFmiR is a freely available web server for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis.
::DEVELOPER
Mohamed Hamed, Christian Spaniol, Maryam Nazarieh, & Volkhard Helms, Chair of Computational Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks.
Hamed M, Spaniol C, Nazarieh M, Helms V.
Nucleic Acids Res. 2015 May 5. pii: gkv418.
:: DESCRIPTION
tigre is an R/Bioconductor package for inference of transcription factor activity and ranking candidate target genes from gene expression time series.
tigreBrowser is a web-based browser for tigre ranking results. It allows easy viewing, sorting and filtering of visualisations of models produced by tigre.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Apr 1;27(7):1026-7. doi: 10.1093/bioinformatics/btr057. Epub 2011 Feb 7.
tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor.
Honkela A1, Gao P, Ropponen J, Rattray M, Lawrence ND.
:: DESCRIPTION
TFpredict is a tool which implements a novel three-step classification method which expects a protein sequence as input and (1) distinguishes transcription factors (TF) from other proteins (Non-TF), (2) predicts the structural superclass of TFs (see TransFac classification), and (3) identifies the DNA-binding domains of TFs. Obviously, the latter two classification steps can only be performed if the given protein sequence corresponds to a TF.
::DEVELOPER
the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2013 Dec 12;8(12):e82238. doi: 10.1371/journal.pone.0082238. eCollection 2013.
TFpredict and SABINE: Sequence-Based Prediction of Structural and Functional Characteristics of Transcription Factors.
Eichner J, Topf F1, Dräger A, Wrzodek C, Wanke D, Zell A.
:: DESCRIPTION
motifbreakR is a package for predicting the disruptiveness Of Single Nucleotide Polymorphisms on transcription factor binding sites.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites.
Coetzee SG, Coetzee GA, Hazelett DJ.
Bioinformatics. 2015 Aug 12. pii: btv470.
:: DESCRIPTION
iTAK is a program to identify plant transcription factors (TFs), transcriptional regulators (TRs) and protein kinases (PKs) from protein or nucleotide sequences and then classify individual TFs, TRs and PKs into different gene families. Identification and classification of TFs and TRs are based on the rules (required and forbidden protein domains of each gene family) described in Perez-Rodriguez et al (2010).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
msCentipede is an algorithm for accurately inferring transcription factor binding sites using chromatin accessibility data (Dnase-seq, ATAC-seq)
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.
Raj A, Shim H, Gilad Y, Pritchard JK, Stephens M.
PLoS One. 2015 Sep 25;10(9):e0138030. doi: 10.1371/journal.pone.0138030.
:: DESCRIPTION
SiTaR (Site Tracking and Recognition) is a novel tool for transcription factor binding site prediction.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
SiTaR: a novel tool for transcription factor binding site prediction.
Fazius E, Shelest V, Shelest E.
Bioinformatics. 2011 Oct 15;27(20):2806-11. doi: 10.1093/bioinformatics/btr492.
:: DESCRIPTION
T-cep is a collection of tools for training a univariate first-order hidden Markov model (HMM) over multiple epigenetic data sets to find combinatorial epigenetic regulation patterns.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Liu Q, Bonneville R, Li T, Jin VX.
Transcription factor-associated combinatorial epigenetic pattern reveals higher transcriptional activity of TCF7L2-regulated intragenic enhancers.
BMC Genomics. 2017 May 12;18(1):375. doi: 10.1186/s12864-017-3764-9. PMID: 28499350; PMCID: PMC5429574.
