>
Tag
> Links tagged with 'gene regulatory networks'

Links tagged with 'gene regulatory networks'

RSS FeedCompact ViewList as XMLList as JSON

Found 27 links

Displaying 15 links

AGRISDatabase Content

http://arabidopsis.med.ohio-state.edu/

Model Organisms > Databases

The Arabidopsis Gene Regulatory Information Server (AGRIS) provides a comprehensive resource for gene regulatory studies in the model plant Arabidopsis thaliana. Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsarabidopsis gene regulatory networks genetic databases genetic promoter regions plant gene expression regulation transcription factors

BioProfiling.deTool Content

http://www.BioProfiling.de/gene_list.

Expression > Gene Set Analysis

BioProfiling.de provides a toolkit for the interpretation of gene or protein lists using enrichment of network based statistical frameworks.

NAR Web Server Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsaniline compounds animals drug discovery factual databases gene regulatory networks genes high-throughput screening assays humans mice nitriles protein interaction mapping protein kinase inhibitors proteins quinolines rats

ConsensusPathDBDatabase Content

http://cpdb.molgen.mpg.de

Human Genome > Databases
Model Organisms > Databases
Protein > Databases

ConsensusPathDB is a meta-database that integrates physical protein interactions, metabolic and signaling reactions and gene regulatory interactions in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. ConsensusPathDB offers different ways of utilizing these integrated interaction data, with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals factual databases gene expression gene regulatory networks genetic databases humans metabolic networks and pathways mice protein interaction mapping signal transduction

COXPRESdbDatabase Content

http://coxpresdb.jp

Expression > Databases
Model Organisms > Databases

COXPRESdb (coexpressed gene database) represents the coexpression relationship for human and mouse. Upgrades include a new comparable coexpression measure, Mutual Rank, five other animal species, rat, chicken, zebrafish, fly and nematoda, and addition of different layers of omics data into the integrated network of genes.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimal models animals gene expression gene expression profiling gene regulatory networks genetic databases humans mice protein interaction mapping rats

CytoscapeTool Content

http://www.cytoscape.org/

Protein > Interactions, Pathways, Enzymes

Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimited files containing mRNA expression profiles. The nodes of the interaction networks can be filtered by such variables as GO annotations and number of interactions.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms archaeal proteins bacteriophage lambda biological models computational biology data mining gene expression profiling gene regulatory networks genomics halobacterium messenger rna neural networks (computer) phenotype protein interaction mapping proteins proteomics software design stochastic processes

DroIDDatabase Content

http://droidb.org/

DNA > Databases
Model Organisms > Databases
Protein > Databases

DroID, the Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. DroID contains genetic interactions and experimentally detected protein-protein interactions curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. Protein interactions are annotated with experimental details and periodically updated confidence scores. The database now includes transcription factor-gene and regulatory RNA-gene interactions. Orthologous gene mappings of Drosophila genes to other organisms are also available to facilitate finding interactions based on gene names and identifiers for a number of common model organisms and humans.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals drosophila drosophila proteins gene expression gene regulatory networks genetic databases insect genes micrornas protein interaction mapping systems integration transcription factors

FANTOMDatabase Content

http://fantom.gsc.riken.jp/4/

Expression > Databases
Human Genome > Databases

The Functional Annotation Of the Mammalian Genome (FANTOM) is a database for the transcriptional network that regulates macrophage differentiation. Data comes from cap analysis of gene expression (CAGE), sequencing mRNA 5'-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP-chip for epigenetic marks and transcription factors.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals cell differentiation gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic transcription genomics humans macrophages mice molecular sequence annotation transcription factors tumor cell line

GeneCATTool Content

http://genecat.mpg.de

Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > Plants

The Gene Co-expression Analysis Tool-box (GeneCAT) is a suite of microarray co-expression analysis tools for plant biology. The platform includes both standard co-expression tools such as gene clustering and expression profiling, as well as tools that combine co-expression analysis with BLAST for functional inferencing. Arabidopsis thaliana and Barley are featured plants.

NAR Web Server Issue 2008
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsarabidopsis gene expression profiling gene regulatory networks glucosyltransferases hordeum lipids oligonucleotide array sequence analysis photosynthesis plant genes sequence alignment

GeneMANIATool Content

http://www.genemania.org

Expression > Gene Set Analysis
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast

GeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.

This content is being maintained by baderg.

NAR Web Server Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms animals computational biology factual databases gene regulatory networks genes genomics humans mice
setsUniversity of Toronto

GraphWebTool Content

http://biit.cs.ut.ee/graphweb/

Expression > Networks

GraphWeb is a web server for biological network analysis and module design using a graphical interface.

NAR Web Server Issue 2008
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagscell cycle proteins gene expression profiling gene regulatory networks humans protein interaction mapping

HLungDBDatabase Content

http://www.megabionet.org/bio/hlung/

Human Genome > Databases

The human lung cancer database (HLungDB) is a database with the integration of the lung cancer-related genes, proteins and miRNAs together with the corresponding clinical information. Currently, we have collected 2585 genes and 212 miRNA with the experimental evidences involved in the different stages of lung carcinogenesis through text mining. The results from analysis of transcription factor-binding motifs, the promoters and the SNP sites for each gene are also included. Genes with epigenetic regulation were also included.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid motifs computational biology gene regulatory networks genetic databases genetic epigenesis humans lung neoplasms micrornas neoplastic cell transformation nucleic acid databases protein databases transcription factors

KaPPA-View4Database Content

http://kpv.kazusa.or.jp/kpv4/

Protein > Databases

KaPPA-View4 is a metabolic pathway database which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. Pathway maps of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and maps generated from their gene classifications are available at KaPPA-View4 KEGG version. Gene co-expression data from the databases ATTED-II, COXPRESdb, CoP and MiBASE for human, mouse, rat, Arabidopsis, rice, tomato and other plants are available.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals gene expression profiling gene regulatory networks genetic databases humans metabolic networks and pathways metabolome mice rats

MAGIATool Content

http://gencomp.bio.unipd.it/magia

Expression > Gene Set Analysis
Expression > Transcript Expression Analysis
RNA > Functional RNAs

miRNA and Genes Integrated Analysis (MAGIA) is a web tool for the integrative analysis of target predictions, miRNA and gene expression data

NAR Web Server Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsgene expression gene expression profiling gene regulatory networks humans messenger rna micrornas

mirConnXTool Content

http://www.benoslab.pitt.edu/mirconnx

Expression > Gene Regulation
Expression > Gene Set Analysis
Expression > Networks

mirConnX is a web server for inferring, displaying and parsing mRNA and microRNA gene regulatory networks. mirConnX combines sequence information with gene expression data analysis to create a disease specific, genome wide regulatory network. Only supports human and mouse.

NAR Web Server Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals disease gene expression profiling gene regulatory networks humans messenger rna mice micrornas transcription factors

Network of Cancer GenesDatabase Content

http://bio.ifom-ieo-campus.it/ncg2

Human Genome > Databases

The Network of Cancer Genes (NCG) collects and integrates data on 736 human genes that are mutated in various types of cancer. For each gene, NCG provides information on duplicability, orthology, evolutionary appearance and topological properties of the encoded protein in a comprehensive version of the human protein-protein interaction network. NCG also stores information on all primary interactors of cancer proteins, thus providing a complete overview of 5357 proteins that constitute direct and indirect determinants of human cancer.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals computational biology gene expression profiling gene regulatory networks genetic databases humans mutation neoplasm genes neoplasms neoplastic gene expression regulation nucleic acid databases plant genome