Rigorous assessment of gene set enrichment tests

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Rigorous assessment of gene set enrichment tests

MOTIVATION Several statistical tests are available to detect the enrichment of differential expression in gene sets. Such tests were originally proposed for analyzing gene sets associated with biological processes. The objective evaluation of tests on real measurements has not been possible as it is difficult to decide a priori, which processes will be affected in given experiments. RESULTS W...

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Gene set enrichment analysis using Wilcoxon tests

Gene set enrichment analysis (GSEA) is typically based on tests derived from the KolmogorovSmirnov, which is underpowered and a need for simpler methods has been identified.[2] The wgsea package contains functions for conducting GSEA using a Wilcoxon test to test for differences in the distribution of p values between SNPs within the gene set under test and a control set of SNPs. The mean of th...

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Extensions to gene set enrichment

MOTIVATION Gene Set Enrichment Analysis (GSEA) has been developed recently to capture changes in the expression of pre-defined sets of genes. We propose number of extensions to GSEA, including the use of different statistics to describe the association between genes and phenotypes of interest. We make use of dimension reduction procedures, such as principle component analysis, to identify gene ...

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Gene set enrichment; a problem of pathways.

Gene Set Enrichment (GSE) is a computational technique which determines whether a priori defined set of genes show statistically significant differential expression between two phenotypes. Currently, the gene sets used for GSE are derived from annotation or pathway databases, which often contain computationally based and unrepresentative data. Here, we propose a novel approach for the generatio...

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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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ژورنال

عنوان ژورنال: Bioinformatics

سال: 2012

ISSN: 1460-2059,1367-4803

DOI: 10.1093/bioinformatics/bts164