GAGE: generally applicable gene set enrichment for pathway analysis
نویسندگان
چکیده
منابع مشابه
Absolute enrichment: gene set enrichment analysis for homeostatic systems
The Gene Set Enrichment Analysis (GSEA) identifies sets of genes that are differentially regulated in one direction. Many homeostatic systems will include one limb that is upregulated in response to a downregulation of another limb and vice versa. Such patterns are poorly captured by the standard formulation of GSEA. We describe a technique to identify groups of genes (which sometimes can be pa...
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Gene set enrichment analysis (GSEA) is a statistical method to determine if predefined sets of genes are differentially expressed in different phenotypes. Predefined gene sets may be genes in a known metabolic pathway, located in the same cytogenetic band, sharing the same Gene Ontology category, or any user-defined set. In microarray experiments where no single gene shows statistically signifi...
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MOTIVATION Assessing functional associations between an experimentally derived gene or protein set of interest and a database of known gene/protein sets is a common task in the analysis of large-scale functional genomics data. For this purpose, a frequently used approach is to apply an over-representation-based enrichment analysis. However, this approach has four drawbacks: (i) it can only scor...
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Among the many applications of microarray technology, one of the most popular is the identification of genes that are differentially expressed in two conditions. A common statistical approach is to quantify the interest of each gene with a p-value, adjust these p-values for multiple comparisons, choose an appropriate cut-off, and create a list of candidate genes. This approach has been criticis...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2009
ISSN: 1471-2105
DOI: 10.1186/1471-2105-10-161