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Links tagged with 'transcriptional regulatory elements'

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Found 25 links

Displaying 15 links

AthaMapDatabase Content

http://www.athamap.de/

Expression > Gene Regulation
Model Organisms > Plants

AthaMap is a genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana

This content is being maintained by Reinhard Hehl.

NAR Web Server Issue 2005
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tagsarabidopsis arabidopsis proteins base sequence binding sites cold temperature computational biology conserved sequence dehydration genetic databases genetic transcription genomics molecular sequence data nucleic acid databases plant dna plant gene expression regulation plant genes plant genome protein binding response elements sequence alignment systems integration transcription factors transcriptional regulatory elements untranslated rna

CEASTool Content

http://ceas.cbi.pku.edu.cn

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.

NAR Web Server Issue 2006
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tagsbinding sites chromatin immunoprecipitation genomics human genome humans oligonucleotide array sequence analysis transcription factors transcriptional regulatory elements

CENTDISTTool Content

http://compbio.ddns.comp.nus.edu.sg/~chipseq/centdist/

Expression > Gene Regulation

CENTDIST is a co-motif scanning program to identify co-transcription factors. CENTDIST ranks co-transcription factors based on their distribution around CHIP-seq peaks.

NAR Web Server Issue 2011
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tagsandrogen receptors binding sites chromatin immunoprecipitation dna sequence analysis humans male prostatic neoplasms transcription factors transcriptional regulatory elements tumor cell line

ChIP-ArrayTool Content

http://wanglab.hku.hk/ChIP-Array

Expression > Gene Regulation

ChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.

NAR Web Server Issue 2011
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tagsanimals binding sites chromatin immunoprecipitation gene expression profiling high-throughput nucleotide sequencing humans mice oligonucleotide array sequence analysis transcription factors transcriptional regulatory elements

DiRETool Content

http://dire.dcode.org

Expression > Gene Regulation

A web server for predicting distant (outside of proximal promoter regions) regulatory elements (DiRE) in higher eukaryotic genomces using gene co-expression data, comparative genomics as well as transcription factor binding site information. DiRE allows users to start analysis with raw microarray expression data.

NAR Web Server Issue 2008
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tagsanimals binding sites gene expression profiling gene expression regulation genetic enhancer elements genetic promoter regions genomics humans transcription factors transcriptional regulatory elements

Ensembl Genome BrowserTool Content

http://www.ensembl.org/

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Model Organisms > Other Organisms

Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.

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tagsanimals bacterial genome base sequence cattle computational biology database management systems dna sequence analysis dogs fungal genome gene expression genetic databases genetic polymorphism genetic variation genome genomics human genome humans invertebrates mice nucleic acid databases nucleic acid regulatory sequences plant genome protein databases proteins rats reference standards rna sequence alignment species specificity synteny systems integration tertiary protein structure transcriptional regulatory elements

FlyFactorSurveyDatabase Content

http://pgfe.umassmed.edu/TFDBS/

Model Organisms > Databases

FlyFactorSurvey is a database of DNA binding specificities for Drosophila transcription factors (TFs) determined using the bacterial one-hybrid system. The database provides to recognition motifs and position weight matrices for TFs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome.

NAR Database Issue 2011
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tagsanimals bacteria binding sites drosophila drosophila proteins genetic databases transcription factors transcriptional regulatory elements two-hybrid system techniques

Genome SurveyorTool Content

http://veda.cs.uiuc.edu/gs

Expression > Gene Regulation
Model Organisms > Fly

Genome Surveyor is a tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser.

NAR Web Server Issue 2011
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tagsanimals binding sites drosophila drosophila melanogaster insect genome transcription factors transcriptional regulatory elements

GenomeTraFaCTool Content

http://genometrafac.cchmc.org/genome-trafac/index.jsp

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

GenomeTraFaC is a comparative genomics based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq gene orthologs.

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tagsanimals base sequence binding sites conserved sequence genomics humans mice micrornas nucleic acid databases transcription factors transcriptional regulatory elements

iCRTool Content

http://210.212.215.199/icr/index.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Interactions, Pathways, Enzymes

Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.

NAR Web Server Issue 2006
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tags5' flanking region bacterial genome bacterial proteins binding sites dna-binding proteins genomics mycobacterium tuberculosis nucleic acid regulatory sequences operon prokaryotic cells regulon sequence alignment serine endopeptidases transcription factors transcriptional regulatory elements

jPREdictorTool Content

http://bibiserv.techfak.uni-bielefeld.de/jpredictor/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

jPREdictor predicts cis-regulatory elements using short motifs that are known to bind regulatory proteins. Predictions are made by searching for clusters of these motifs, and weighting these clusters by applying a positive or negative training sets to score the sequence.

NAR Web Server Issue 2006
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tagsanimals binding sites drosophila melanogaster drosophila proteins genomics response elements transcription factors transcriptional regulatory elements

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

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

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

MicroFootPrinterTool Content

http://bio.cs.washington.edu/MicroFootPrinter.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence homology animals archaeal genome bacterial genome computational biology conserved sequence dna footprinting dna sequence analysis fish proteins fos genes genetic promoter regions genomics growth hormone humans insulin interleukin-3 introns metallothionein multigene family myc genes nucleic acid databases nucleic acid regulatory sequences nucleic acid sequence homology phylogeny regulator genes transcriptional regulatory elements

MoD ToolsTool Content

http://159.149.109.16/modtools/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs

Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions from homologous genes; and RNA profile, a tool for secondary structure motif discovery in RNA sequences.

NAR Web Server Issue 2006
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tagsbinding sites dna sequence analysis gene expression regulation nucleic acid conformation nucleic acid sequence homology ribonucleic acid regulatory sequences rna sequence analysis transcription factors transcriptional regulatory elements untranslated rna

ORegAnnoDatabase Content

http://www.oreganno.org/

DNA > Annotations
DNA > Databases
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Human Genome > Annotations
Human Genome > Sequence Polymorphisms

The Open REGulatory ANNOtation database (ORegAnno) is a collection of literature-curated regulatory regions, transcription factor binding sites (TFBS) and regulatory mutations.

This content is being maintained by obigriffith.

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tagsanimals binding sites database management systems documentation gene expression regulation genetic databases genetic promoter regions genetic variation humans natural language processing nucleic acid databases periodicals as topic protein binding transcription factors transcriptional regulatory elements