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GeneTrail--advanced gene set enrichment analysis.

Nucleic acids research | Jul 16, 2007

We present a comprehensive and efficient gene set analysis tool, called 'GeneTrail' that offers a rich functionality and is easy to use. Our web-based application facilitates the statistical evaluation of high-throughput genomic or proteomic data sets with respect to enrichment of functional categories. GeneTrail covers a wide variety of biological categories and pathways, among others KEGG, TRANSPATH, TRANSFAC, and GO. Our web server provides two common statistical approaches, 'Over-Representation Analysis' (ORA) comparing a reference set of genes to a test set, and 'Gene Set Enrichment Analysis' (GSEA) scoring sorted lists of genes. Besides other newly developed features, GeneTrail's statistics module includes a novel dynamic-programming algorithm that improves the P-value computation of GSEA methods considerably. GeneTrail is freely accessible at http://genetrail.bioinf.uni-sb.de.

Pubmed ID: 17526521 RIS Download

Mesh terms: Animals | Computational Biology | Database Management Systems | Databases, Genetic | Gene Expression Regulation | Genes, Fungal | Genome | Genomics | Humans | Internet | Models, Genetic | Models, Statistical | Programming Languages | Proteomics | Software | User-Computer Interface

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Plant enzymes and biochemical pathways database

The Plant Metabolic Network (PMN) is a collaborative project among databases and biochemists with a common goal to build a broad network of plant metabolic pathway databases. A central feature of the PMN is PlantCyc, a comprehensive plant biochemical pathway database, containing curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism. The central goal of the Plant Metabolic Network (PMN) is to bring together biochemical pathway databases and research communities focused on plant metabolism. PMN will generate an infrastructure for drawing together diverse sources of plant metabolism information.

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IntAct

Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available.

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