> Tag > Links tagged with 'transcription factors'

Links tagged with 'transcription factors'

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TransmiRDatabase Content

http://cmbi.bjmu.edu.cn/transmir [open in a new window]

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Protein > Databases

The TF-miRNA regulatory database (TransmiR) contains transcription factors and miRNAs along with regulatory pairs. References to the published literature (PubMed ID) information about the organism in which the relationship was found, whether the TFs and miRNAs are involved with tumors, miRNA function annotation and miRNA-associated disease annotation are also included. TransmiR provides a user-friendly interface by which interested parties can easily retrieve TF-miRNA regulatory pairs by searching for either a miRNA or a TF.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
TransmiR: a transcription factor-microRNA regulation database201037
NAR Database Issue 2010
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tagsalgorithms animals computational biology gene regulatory networks genetic databases humans micrornas nucleic acid databases phenotype protein databases pubmed transcription factors

VAMPIRETool Content

http://genome.ucsd.edu/microarray/ [open in a new window]

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Expression > Transcript Expression Analysis

VAMPIRE is a collection of Java tools designed to perform Bayesian statistical analysis of gene expression array data.

links directory index: 111
TitlePublication YearGoogle Scholar Citation Count
VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data200554
Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes200457
NAR Web Server Issue 2005
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tags3t3-l1 cells adipocytes algorithms animals bayes theorem biological models database management systems dimethyl sulfoxide gene expression profiling gene expression regulation genetic variation mice oligonucleotide array sequence analysis statistical data interpretation statistical models thiazolidinediones transcription factors

VisANTTool Content

http://visant.bu.edu/ [open in a new window]

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Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Networks & Interactions, Pathways and Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

links directory index: 372
TitlePublication YearGoogle Scholar Citation Count
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology200947
Towards zoomable multidimensional maps of the cell200749
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction200754
VisANT: data-integrating visual framework for biological networks and modules2005107
VisANT: an online visualization and analysis tool for biological interaction data2004115
NAR Web Server Issue 2005NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques

VOMBATTool Content

https://www2.informatik.uni-halle.de:8443/VOMBAT/faces/pages/choose.jsp [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

VOMBAT predicts transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order BAyesian Trees.

links directory index: 99
TitlePublication YearGoogle Scholar Citation Count
VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees20069
Identification of transcription factor binding sites with variable-order Bayesian networks200590
NAR Web Server Issue 2006
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tagsalgorithms artificial intelligence bayes theorem binding sites chemical models computer simulation genomics markov chains molecular models protein binding protein databases protein sequence analysis sequence alignment statistical models structure-activity relationship transcription factors transcriptional regulatory elements

Web WeederTool Content

http://159.149.109.9/modtools/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Server which identifies conserved motifs within sets of related regulatory DNA sequences, which are likely to be transcription factor binding sites. The interface will automatically conduct several runs using different parameters and output a summary.

links directory index: 294
TitlePublication YearGoogle Scholar Citation Count
Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes2004294
NAR Web Server Issue 2004
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tagsalgorithms binding sites computational biology dna gene expression regulation nucleic acid regulatory sequences transcription factors

WebMOTIFSTool Content

http://fraenkel.mit.edu/webmotifs/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features

WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.

links directory index: 80
TitlePublication YearGoogle Scholar Citation Count
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches200729
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data200651
NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs animals automated pattern recognition automation base sequence bayes theorem binding sites chromatin immunoprecipitation cluster analysis computational biology conserved sequence dna dna sequence analysis gene expression profiling humans mice molecular sequence data protein binding saccharomyces cerevisiae sequence alignment transcription factors

WormBaseDatabase Content

http://www.wormbase.org [open in a new window]

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Model Organisms > Databases
Model Organisms > Worm

WormBase is a data repository for nematode biology. WormBase has expanded to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes.

links directory index: 103
TitlePublication YearGoogle Scholar Citation Count
WormBase 2012: more genomes, more data, new website20124
WormBase: a comprehensive resource for nematode research201099
NAR Database Issue 2010
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tagsalleles animals caenorhabditis caenorhabditis elegans computational biology genetic databases nucleic acid databases phenotype protein databases tertiary protein structure transcription factors

WormBaseDatabase Content

http://www.wormbase.org/ [open in a new window]

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Model Organisms > Worm

Repository of mapping, sequencing and phenotypic information about C. elegans and C. briggsae.

links directory index: 206
TitlePublication YearGoogle Scholar Citation Count
WormBase: a comprehensive resource for nematode research201099
WormBase: a cross-species database for comparative genomics2003107
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tagsalleles animals base sequence caenorhabditis caenorhabditis elegans computational biology data collection expressed sequence tags gene expression genetic databases genomics helminth dna helminth genes helminth rna high-throughput nucleotide sequencing information storage and retrieval intergenic dna internet molecular sequence annotation neurons nucleic acid databases nucleic acid sequence homology open reading frames phenotype protein databases quality control rna interference single nucleotide polymorphism software tertiary protein structure transcription factors

YEASTRACTDatabase Content

http://www.yeastract.com [open in a new window]

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Model Organisms > Databases

The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT) is a curated repository of regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. EASTRACT allows the identification of documented or potential transcription regulators of a given gene and of documented or potential regulons for each transcription factor. It also renders possible the comparison between DNA motifs and the transcription factor binding sites described in the literature. YEASTRACT provides a set of queries to search and retrieve important biological information from the gathered data and to predict transcription regulation networks in yeast from data emerging from gene-by-gene analysis or global approaches.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface201119
NAR Database Issue 2011
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tagsbinding sites fungal gene expression regulation genetic databases genetic transcription saccharomyces cerevisiae saccharomyces cerevisiae proteins transcription factors

YMF 3.0Tool Content

http://wingless.cs.washington.edu/YMF/YMFWeb/YMFInput.pl [open in a new window]

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DNA > Structure and Sequence Feature Detection

YMF 3.0 (Yeast Motif Finder) is a tool that identifies good candidates for transcription factor binding sites by searching for statistically overrepresented motifs. Multiple organisms are supported including human, yeast, worm, plants, and microbes.

links directory index: 181
TitlePublication YearGoogle Scholar Citation Count
YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation2003181
NAR Web Server Issue 2003
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tagsalgorithms binding sites dna sequence analysis genetic promoter regions mycobacterium tuberculosis nucleic acid regulatory sequences saccharomyces cerevisiae statistical data interpretation transcription factors

YPADatabase Content

http://ypa.ee.ncku.edu.tw/ [open in a new window]

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DNA > Databases
Model Organisms > Databases

The Yeast Promoter Atlas (YPA) database collects promoter features in Saccharomyces cerevisiae. YPA integrates nine kinds of promoter features including promoter sequences, genes' transcription boundaries-transcription start sites (TSSs), five prime untranslated regions (5'-UTRs) and three prime untranslated regions (3'UTRs), TATA boxes, transcription factor binding sites (TFBSs), nucleosome occupancy, DNA bendability, transcription factor (TF) binding, TF knockout expression and TF-TF physical interaction. In YPA, various promoter features can be accessed in a centralized and organized platform.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
YPA: an integrated repository of promoter features in Saccharomyces cerevisiae20113
NAR Database Issue 2011
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tagsbinding sites genetic promoter regions nucleic acid databases saccharomyces cerevisiae systems integration transcription factors

ZiFiTTool Content

http://bindr.gdcb.iastate.edu/ZiFiT/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences. ZiFiT has been updated to integrate additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database of engineered ZFPs, and direct query of NCBI BLAST servers for identification of potential off-target sites within a host genome.

links directory index: 76
TitlePublication YearGoogle Scholar Citation Count
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool201018
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool200758
NAR Web Server Issue 2007NAR Web Server Issue 2010
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tagsbinding sites computational biology deoxyribonucleases dna sequence analysis dna-binding proteins humans protein conformation protein engineering secondary protein structure tertiary protein structure transcription factors zinc fingers

Zinc Finger ToolsTool Content

http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Zinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.

links directory index: 984
TitlePublication YearGoogle Scholar Citation Count
Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases2006135
Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors2005117
Scanning the human genome with combinatorial transcription factor libraries200394
Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors2001218
Insights into the molecular recognition of the 5'-GNN-3' family of DNA sequences by zinc finger domains2000113
Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences1999307
NAR Web Server Issue 2006
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tagsamino acid sequence animals base sequence binding sites biomolecular nuclear magnetic resonance cell line combinatorial chemistry techniques computer simulation deoxyribonuclease i deoxyribonucleases dna dna primers dna sequence analysis dna-binding proteins down-regulation drug design enzyme-linked immunosorbent assay epidermal growth factor receptor erbb genes erbb-1 genes erbb-2 genes erbb-2 receptor erbb-3 receptor flow cytometry gene expression profiling gene expression regulation gene library gene targeting genetic promoter regions genetic transcription green fluorescent proteins histidine human genome humans kidney luminescent proteins lysine mice molecular cloning molecular models molecular sequence data mutation nucleic acid conformation oligonucleotides peptide library pliability polymerase chain reaction protein conformation protein engineering proteomics recombinant proteins reporter genes retroviridae secondary protein structure sequence analysis site-directed mutagenesis substrate specificity tertiary protein structure transcription factors transfection up-regulation x-ray crystallography zinc fingers

zPicture and multi-zPictureTool Content

http://zpicture.dcode.org/ [open in a new window]

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Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

zPicture (pairwise alignment) and multi-zPicture (multiple alignment) are web-based sequence alignment tools based on the blastz alignment program. Alignments from zPicture can be automatically submitted to rVista.

links directory index: 92
TitlePublication YearGoogle Scholar Citation Count
zPicture: dynamic alignment and visualization tool for analyzing conservation profiles200492
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tagsanimals bacterial dna bacterial genome binding sites conserved sequence humans mice mycobacterium leprae mycobacterium tuberculosis nucleic acid sequence homology sequence alignment transcription factors

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