Networks

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

Found 29 links

Displaying 15 links

BabelomicsTool Content

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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.

BioMet ToolboxTool Content

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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

DIANA miRPathTool Content

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DIANA miRPath v2.0 is a web-based computational tool that identifies potentially altered molecular pathways by the expression of a single or multiple microRNAs.

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ENDEAVOURTool Content

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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.

Enrichment Map Cytoscape PluginTool Content

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A Cytoscape plugin for functional enrichment visualization. Gene-sets, such as pathways and Gene Ontology terms, are organized into a network (i.e. the "enrichment map"). In this way, mutually overlapping gene-sets cluster together, making interpretation easier. Enrichment Map also enables the comparison of two different enrichment results in the same map.

This content is being maintained by baderg.

GeneCodis3Tool Content

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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. Noisy and redundant output data has been removed from enrichment results, and greater comparative analyses are possible.

GENIESTool Content

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The Gene Network Inference Engine based on Supervised Analysis (GENIES) webserver predicts potential functional associations between genes, based on other genomic data or high-throughput experimental data such as phylogenetic profiles and gene expression profiles.

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GenoCADTool Content

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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.

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GraphWebTool Content

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

GRNsight: a Web Application and Service for Visualizing Models of Small- to Medium-scale Gene Regulatory NetworksResource Content

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GRNsight allows users to upload Excel spreadsheets containing an adjacency matrix and automatically creates and displays a graph of the gene regulatory network model. The application colors the edges and adjusts their thickness based on the sign (activation or repression) and the strength (magnitude) of the regulatory relationship, respectively. GRNsight then allows the user to modify the graph in order to define the best visual layout for the network.

This content is being maintained by kdahlquist.

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IMPTool Content

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Integrative Multi-species Prediction (IMP) is a webserver that enables biologists to analyze their experimental results in the functional context of gene networks from multiple organisms.

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IntScoreTool Content

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INtScore is a web tool for confidence scoring of biological interactions. Individual interactions are weighted according to the likelihood that they actually take place in the cell, and can be used to filter out false positives.

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KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

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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.

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