> Tag > Links tagged with 'gene expression regulation'

Links tagged with 'gene expression regulation'

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Found 67 links

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ARGOTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/argo/ [open in a new window]

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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.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters200514
NAR Web Server Issue 2005
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tagsalgorithms binding sites eukaryotic cells gene expression regulation genetic promoter regions genomics transcription factors

ASIANTool Content

http://eureka.cbrc.jp/asian/ [open in a new window]

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Expression > Transcript Expression Analysis

ASIAN (Automatic System for Inferring a Network) is a server for inferring regulatory networks from gene expression profiles that combines cluster analysis, regression analysis, and graphical Gaussian modeling.

links directory index: 287
TitlePublication YearGoogle Scholar Citation Count
ASIAN: a web server for inferring a regulatory network framework from gene expression profiles200523
ASIAN: a website for network inference200417
Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling2002186
Statistical estimation of cluster boundaries in gene expression profile data200161
NAR Web Server Issue 2005
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tagsanalysis of variance bayes theorem biological models cluster analysis computational biology computer simulation factual databases fungal genes gene expression gene expression profiling gene expression regulation genetic models oligonucleotide array sequence analysis proteome regression analysis saccharomyces cerevisiae signal transduction statistical data interpretation statistical models

BioMet ToolboxTool Content

http://www.sysbio.se/BioMet [open in a new window]

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Expression > Networks
Expression > Transcript Expression Analysis
Other Molecules > Metabolites
Protein > Networks & Interactions, Pathways and Enzymes

The BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rates and metabolic production rates. Files for model organisms are included.

This content is being maintained by marija.

links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
BioMet Toolbox: genome-wide analysis of metabolism201017
NAR Web Server Issue 2010
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tagsalgorithms ethanol gene expression profiling gene expression regulation genome glucose metabolic networks and pathways protein interaction mapping transcription factors

BioProspectorTool Content

http://robotics.stanford.edu/~xsliu/BioProspector/ [open in a new window]

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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.

links directory index: 702
TitlePublication YearGoogle Scholar Citation Count
A suite of web-based programs to search for transcriptional regulatory motifs200432
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes2001670
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

BioverseTool Content

http://bioverse.compbio.washington.edu/ [open in a new window]

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DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

links directory index: 95
TitlePublication YearGoogle Scholar Citation Count
Functional annotation from predicted protein interaction networks200537
BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes200513
Enhanced functional information from predicted protein networks200420
Bioverse: Functional, structural and contextual annotation of proteins and proteomes200325
NAR Web Server Issue 2005NAR Web Server Issue 2003
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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

BSQATool Content

http://www.beespace.uiuc.edu/QuestionAnswer [open in a new window]

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Literature > Text Mining and Semantics
Model Organisms > Fly

BeeSpace Question/Answering (BSQA) system is a web server that performs integrated text mining for insect biology, covering diverse aspects from molecular interactions of genes to insect behavior. BSQA recognizes a number of entities and relations in Medline documents about the model insect, Drosophila melanogaster.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects20104
NAR Web Server Issue 2010
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tagsanimal behavior animals data mining drosophila melanogaster gene expression regulation homeodomain proteins insect genes insects systems integration trans-activators

CARRIETool Content

http://zlab.bu.edu/CARRIE-web [open in a new window]

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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.

links directory index: 30
TitlePublication YearGoogle Scholar Citation Count
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis200430
Questions and answers about AIDS.19920
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

CompareProspectorTool Content

http://compareprospector.stanford.edu/ [open in a new window]

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

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.

links directory index: 164
TitlePublication YearGoogle Scholar Citation Count
A suite of web-based programs to search for transcriptional regulatory motifs200432
Eukaryotic regulatory element conservation analysis and identification using comparative genomics2004132
NAR Web Server Issue 2004
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tagsalgorithms animals binding sites caenorhabditis caenorhabditis elegans conserved sequence dna eukaryotic cells fungal genes gene expression regulation genes genetic transcription genomics helminth genes humans mice nucleic acid regulatory sequences regulator genes saccharomyces saccharomyces cerevisiae schizosaccharomyces transcription factors

CONREALTool Content

http://conreal.niob.knaw.nl/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

links directory index: 125
TitlePublication YearGoogle Scholar Citation Count
CONREAL web server: identification and visualization of conserved transcription factor binding sites200541
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting200484
NAR Web Server Issue 2005
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tagsalgorithms animals base sequence binding sites conserved sequence dna footprinting dna sequence analysis dna-binding proteins gene expression regulation genetic promoter regions hepatocyte nuclear factor 3-beta humans mice nuclear proteins nucleic acid regulatory sequences nucleic acid sequence homology phylogeny rats sequence alignment takifugu transcription factors zebrafish

CREMETool Content

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

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Other Resources

CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.

links directory index: 65
TitlePublication YearGoogle Scholar Citation Count
CREME: Cis-Regulatory Module Explorer for the human genome200465
NAR Web Server Issue 2004
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tagsbinding sites computational biology gene expression regulation genetic promoter regions human genome humans transcription factors

CRSDDatabase Content

http://140.120.213.10:8080/crsd/main/home.jsp [open in a new window]

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

Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).

links directory index: 28
TitlePublication YearGoogle Scholar Citation Count
CRSD: a comprehensive web server for composite regulatory signature discovery200628
NAR Web Server Issue 2006
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tags3' untranslated regions binding sites cluster analysis gene expression profiling gene expression regulation genetic databases genetic promoter regions genomics humans micrornas oligonucleotide array sequence analysis transcription factors

DCODE.ORGResource Content

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

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Human Genome > Other Resources
Sequence Comparison > Comparative Genomics

The dcode.org website provides access to tools for comparative genomic analyses developed by the Comparative Genomics Center at the Lawerence Livermore National Laboratory. Tools include: zPicture, Mulan, eShadow, rVista, CREME, and the ECR Browser.

links directory index: 32
TitlePublication YearGoogle Scholar Citation Count
Dcode.org anthology of comparative genomic tools200532
NAR Web Server Issue 2005
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tagsbase sequence binding sites computational biology gene expression regulation genetic promoter regions genomics humans molecular evolution nucleic acid regulatory sequences phylogeny sequence alignment transcription factors

DIANA-microTTool Content

http://www.microrna.gr/microT [open in a new window]

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Expression > Gene Regulation
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Worm
RNA > Functional RNAs

The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.

links directory index: 110
TitlePublication YearGoogle Scholar Citation Count
DIANA-microT web server: elucidating microRNA functions through target prediction2009110
NAR Web Server Issue 2009NAR Web Server Issue 2011
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tagsalgorithms binding sites gene expression regulation messenger rna micrornas rna sequence analysis

DiRETool Content

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

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Expression > Gene Regulation
Expression > Transcript Expression Analysis

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.

links directory index: 31
TitlePublication YearGoogle Scholar Citation Count
DiRE: identifying distant regulatory elements of co-expressed genes200831
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

ENCODE DCCDatabase Content

http://encodeproject.org/ENCODE/ [open in a new window]

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DNA > Databases
Expression > Databases
Protein > Databases
RNA > Databases

The ENCODE project has a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) serves as the central repository for ENCODE data. The DCC contains a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser. ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay.

links directory index: 122
TitlePublication YearGoogle Scholar Citation Count
ENCODE whole-genome data in the UCSC genome browser (2011 update)201136
ENCODE whole-genome data in the UCSC Genome Browser201086
NAR Database Issue 2010NAR Database Issue 2011
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tagsanimals computational biology gene expression regulation genetic databases genomics human genome humans mice nucleic acid databases sequence alignment tumor cell line

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