Enrichment analysis is normally used to identify relevant biological features that can be used to describe a set of genes under analysis that, for example, share a common expression profile. In this article we propose the exploitation of enrichment analysis for a different purpose: the evaluation of a disease prognosis. With this application of enrichment analysis we expect to identify clinical...

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, TR...

: Enrichment analysis is well established in the field of transcriptomics, where it is used to identify relevant biological features that characterize a set of genes obtained in an experiment.This article proposes the application of enrichment analysis as a first step in a disease prognosis methodology, in particular of diseases with a strong genetic component. With this analysis the objective ...

We have developed a biologist-friendly, Java GUI application (GoBean) for GO term enrichment analysis. It was designed to be a comprehensive and flexible GUI tool for GO term enrichment analysis, combining the merits of other programs and incorporating extensive graphic exploration of enrichment results. An intuitive user interface with multiple panels allows for extensive visual scrutiny of an...

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...

Disease Ontology (DO) aims to provide an open source ontology for the integration of biomedical data that is associated with human disease. We developed DOSE package to promote the investigation of diseases. DOSE provides five methods including Resnik, Lin, Jiang, Rel and Wang for measuring semantic similarities among DO terms and gene products; Hypergeometric model and gene set enrichment anal...

UNLABELLED While many tools exist for performing enrichment analysis of transcriptomic and proteomic data in order to interpret them in biological terms, almost no equivalent tools exist for metabolomic data. We present Metabolite Biological Role (MBRole), a web server for carrying out over-representation analysis of biological and chemical annotations in arbitrary sets of metabolites (small ch...

MOTIVATION Many studies have investigated the differential expression of microRNAs (miRNAs) in disease states and between different treatments, tissues and developmental stages. Given a list of perturbed miRNAs, it is common to predict the shared pathways on which they act. The standard test for functional enrichment typically yields dozens of significantly enriched functional categories, many ...

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...

Similar to the development of gene set enrichment and gene regulatory network analysis tools over a decade ago, microRNA enrichment tools are currently gaining importance. Building on our experience with the gene set analysis toolkit GeneTrail, we implemented the miRNA Enrichment Analysis and Annotation tool (miEAA). MiEAA is a web-based application that offers a variety of commonly applied sta...