> > Gene Regulation

Gene Regulation

This section contains links to tools and resources for predicting gene regulation, such as promoter analysis. It also contains tools and resources for evaluation of the regulatory role of miRNA and other functional RNA molecules.

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Found 133 links

Displaying 15 links

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

NAR Web Server Issue 2003
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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

AntiHunter 2.0Tool Content

http://bio.ifom-ieo-campus.it/antihunter

Expression > Gene Regulation
Expression > cDNA, EST, SAGE

AnitHunter 2.0 is a tool to detect potential EST antisense transcripts within a given genomic region from the analysis of BLAST output.

NAR Web Server Issue 2005
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tagsalgorithms antisense rna dna sequence analysis expressed sequence tags genetic databases sequence alignment time factors

ARGOTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/argo/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

ARGO is a tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes.

NAR Web Server Issue 2005
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tagsalgorithms binding sites eukaryotic cells gene expression regulation genetic promoter regions genomics transcription factors

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

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

NAR Web Server Issue 2005NAR Web Server Issue 2006NAR Web Server Issue 2008NAR Web Server Issue 2010
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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

BEARRTool Content

http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Human Genome > Other Resources
Model Organisms > Mouse and Rat

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

NAR Web Server Issue 2004
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tagsbinding sites dna dna sequence analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis software design transcription factors

BioBayesNetTool Content

http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/

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

BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence automated pattern recognition bayes theorem binding sites chemical models computational biology computer simulation dna sequence analysis genetic models molecular models molecular sequence data protein binding protein conformation protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship transcription factors

BioProspectorTool Content

http://robotics.stanford.edu/~xsliu/BioProspector/

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

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.

NAR Web Server Issue 2004
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tagsalgorithms bacillus subtilis base sequence binding sites carrier proteins conserved sequence cyclic amp receptor protein dna escherichia coli gene expression profiling gene expression regulation genetic models genetic transcription markov chains nucleic acid regulatory sequences oligonucleotide array sequence analysis rap1 gtp-binding proteins regulator genes saccharomyces cerevisiae sequence alignment tata box transcription factors

CARRIETool Content

http://zlab.bu.edu/CARRIE-web

Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.

NAR Web Server Issue 2004
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tagsacquired immunodeficiency syndrome binding sites computational biology dna female gene expression profiling gene expression regulation genetic promoter regions genetic transcription hiv hiv infections humans male newborn infant nucleic acid regulatory sequences nurses oligonucleotide array sequence analysis physicians pregnancy transcription factors

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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ChinookTool Content

http://www.bcgsc.bc.ca/chinook/

Computer Related > Web Services
DNA > DNA and Genomic Analysis
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

Chinook is a peer-to-peer (P2P) service for the discovery, use and assessment of bioinformatics programs. Chinook Online allows researchers to connect and run distributed bioinformatics programs using a web application.

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tagsbenchmarking biomedical technology assessment computational biology computing methodologies software validation

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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CisMolsTool Content

http://cismols.cchmc.org/

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

CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.

NAR Web Server Issue 2005
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tagsbase sequence binding sites conserved sequence gene expression regulation genomics response elements transcription factors

cisREDDatabase Content

http://www.cisred.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

cisRED is a database system for genome-scale computational discovery of regulatory elements.

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tagsanimals computational biology genetic promoter regions genomics nucleic acid databases response elements

Tags associated with subcategory 'Expression/Gene Regulation'

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