Gene Set Analysis

Tools for evaluation of gene sets generated through any number of expression technologies.

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BioMet Toolbox 2.0Tool Content

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BioMet Toolbox 2.0 is a web server for genome-wide analysis of metabolism and omics data. BioMet Toolbox exploits the capabilites of metabolic networks described in genome scale models using flux analysis and random sampling, and gene set analysis and basic microarray analysis, thereby providing an integrated analysis to identify coregulated subnetwork structures within the metabolic network and also for identifying statistically significant gene sets enabling biological interpretation.

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CCancerDatabase Content

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CCancer is an automatically collected database of gene lists reported in various studies. The current coverage is 3369 gene lists from 2644 papers. Enrichment analysis reports intersecting gene lists with an inputted gene list.

EdenaTool Content

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Edena is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer.

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ErmineJTool Content

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ErmineJ is software for the analysis of functionally interesting patterns in large gene lists drawn from gene expression profiling data or other high-throughput genomics studies. It can be used by biologists with no bioinformatics background to conduct sophisticated analyses of gene sets with multiple methods. It allows users to assess whether microarray data or other gene lists are enriched for a particular pathway or gene class.

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EvoCorTool Content

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EvoCor is a web server for predicting functionally related genes using phylogenetic and expression profiles.

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FIDEATool Content

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FIDEA is a web tool for the functional interpretation of differential gene expression analysis. Multiple model organisms are represented.

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G-SESAMETool Content

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G-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.

GendooTool Content

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Gene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to OMIM data. This approach assists in interpreting -omic data for its molecular and clinical aspects.

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Gene Array AnalyzerTool Content

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The Gene Array Analyzer (GAA) allow to process CEL files from GeneChip® Gene 1.0 ST Arrays. Various processing steps and visualizations are implemented to identify alternative splicing events. Three simple steps have to be performed to submit a set of CEL files. After the processing is completed the results can be viewed in the browser.

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.

GeneMANIATool Content

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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.

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GeneManiaTool Content

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The GeneMANIA Cytoscape plugin brings fast gene function prediction capabilities to the desktop. GeneMANIA identifies the most related genes to a query gene set using a guilt-by-association approach. The plugin uses a large database of functional interaction networks from multiple organisms and each related gene is traceable to the source network used to make the prediction. Users may add their own interaction networks and expression profile data to complement or override the default data.

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