> > Networks

Networks

This section contains links for integrating and analyzing a variety of biological data sets.

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Found 16 links

Displaying 15 links

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

BioMet ToolboxTool Content

http://www.sysbio.se/BioMet

Expression > Networks
Expression > Transcript Expression Analysis
Other Molecules > Metabolites
Protein > Interactions, Pathways, 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.

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

CPA - Comparative Pathway AnalyzerTool Content

https://www.cebitec.uni-bielefeld.de/groups/brf/software/cpa/index.html

Expression > Networks
Model Organisms > Microbes
Protein > Interactions, Pathways, Enzymes

The Comparative Pathway Analyzer (CPA) is a web tool for comparative metabolic network analysis. The differences in metabolic reaction content between two sets of organisms are computed and displayed on KEGG pathway maps.

NAR Web Server Issue 2008
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tagscluster analysis factual databases metabolic networks and pathways

ENDEAVOURTool Content

http://www.esat.kuleuven.be/endeavour

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.

This content is being maintained by ltranche.

NAR Web Server Issue 2008
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tagsalgorithms animal models animals caenorhabditis elegans cell differentiation chromosome mapping computational biology drosophila melanogaster gene expression regulation genes genetic models genetic predisposition to disease humans mice rats roc curve sensitivity and specificity statistical models zebrafish

GeneCodisTool Content

http://genecodis.dacya.ucm.es

Computer Related > Web Services
DNA > Annotations
Expression > Gene Set Analysis
Expression > Networks

Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations.

NAR Web Server Issue 2009
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tagsanimals cattle gene expression regulation genes humans mice micrornas rats systems integration transcription factors

GenoCADTool Content

http://www.genocad.org

DNA > Tools For the Bench
Expression > Networks
Expression > Protein Expression

GenoCAD is a web-based application for designing protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks. Users can download the designed sequence for synthesis or further analysis. Users can also create personal accounts and thus can customize their workspace.

This content is being maintained by peccoud.

NAR Web Server Issue 2009
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tagsbase sequence chromosome mapping computer simulation dna gene database genetic code genetic engineering genetic models genomic islands nucleic acid databases reference standards synthetic genes

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
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tagscell cycle proteins gene expression profiling gene regulatory networks humans protein interaction mapping

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/

Expression > Networks
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

NAR Web Server Issue 2008
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tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

MADNetTool Content

http://www.bioinfo.hr/madnet

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Microarray Database Network (MADNet) is a data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. Data is integrated with information from NCBI, KEGG TRANSFAC and DrugBank.

NAR Web Server Issue 2008
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tagsgene expression profiling genetic databases metabolic networks and pathways oligonucleotide array sequence analysis signal transduction systems integration

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
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NeATTool Content

http://rsat.ulb.ac.be/neat/

Expression > Networks

Network Analysis Tools (NeAT) is a suite of tools for the analysis of biological networks, clusters, classes and pathways. Tools are available as web services for integration into programmatic work flows.

NAR Web Server Issue 2008
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tagscluster analysis gene expression regulation metabolic networks and pathways oligonucleotide array sequence analysis protein interaction mapping signal transduction

ProdoNetTool Content

http://www.prodonet.tu-bs.de

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > Microbes

A web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps.

NAR Web Server Issue 2008
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tagsbacteria bacterial genes bacterial proteins gene expression profiling gene regulatory networks membrane proteins metabolic networks and pathways operon pseudomonas aeruginosa regulon

SNPsynTool Content

http://snpsyn.biolab.si

Expression > Gene Set Analysis
Expression > Networks
Human Genome > Sequence Polymorphisms

SNPsyn is a tool for the discovery of synergistic pairs of SNPs from large genome-wide case-control association studies data on complex diseases. The SNPsyn web server receives GWAS data submissions, invokes the interaction analysis and returns results. The user can explore details on identified SNP-SNP pairs, perform gene set enrichment analysis and interact with the constructed SNP synergy network.

NAR Web Server Issue 2011
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SPEEDTool Content

http://speed.sys-bio.net/

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

Signaling Pathway Enrichment using Experimental Datasets (SPEED) is a web server for enrichment of signaling pathways responsible for gene expression changes.

NAR Web Server Issue 2010
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tagsalgorithms ccaat-enhancer-binding proteins gene expression profiling gene expression regulation genetic databases humans mutation myeloid leukemia signal transduction transcription factors tumor cell line

ToppGene SuiteTool Content

http://toppgene.cchmc.org

Expression > Gene Set Analysis
Expression > Networks

ToppGene has a suite of tools for gene list functional enrichment, gene prioritization and identification of novel disease genes in an interactome.

NAR Web Server Issue 2009
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tagsanimals disease genes humans mice protein interaction mapping proteins

Tags associated with subcategory 'Expression/Networks'

humans gene expression profiling genes protein interaction mapping transcription factors animals gene expression regulation metabolic networks and pathways mice algorithms systems integration genetic models signal transduction gene regulatory networks genetic databases rats genome computer simulation computational biology chromosome mapping oligonucleotide array sequence analysis regulon male operon multiprotein complexes pseudomonas aeruginosa fungal genes cell cycle database management systems drosophila testis metabolism genetic transcription dna sequence analysis two-hybrid system techniques genomics phylogeny systems biology sequence alignment proteomics three-dimensional imaging software design helminth proteins helminth genes macromolecular substances protein databases saccharomyces cerevisiae proteins saccharomyces cerevisiae proteome membrane proteins bacterial proteins gene database dna base sequence genetic code genetic engineering molecular structure molecular sequence data nucleic acid databases genomic islands ligands japan genetic predisposition to disease drosophila melanogaster cell differentiation animal models roc curve sensitivity and specificity gene expression amino acid sequence zebrafish statistical models pharmaceutical preparations protein binding glucose tumor cell line myeloid leukemia mutation sequence homology reference standards proteins disease micrornas synthetic genes ccaat-enhancer-binding proteins ethanol cluster analysis bacterial genes bacteria cattle factual databases cell cycle proteins caenorhabditis elegans biological models binding sites artificial intelligence