Differential Gene Set Enrichment Analysis: a statistical approach to quantify the relative enrichment of two gene sets
نویسندگان
چکیده
منابع مشابه
Integration of Differential Gene-combination Search and Gene Set Enrichment Analysis: A General Approach
Motivation: Gene Set Enrichment Analysis (GSEA) and its variations aim to discover collections of genes that show moderate but coordinated differences in expression. However, such techniques may be ineffective if many individual genes in a phenotype-related gene set have weak discriminative power. A potential solution is to search for combinations of genes that are highly differentiating even w...
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BACKGROUND Gene set enrichment analysis (GSEA) is an analytic approach which simultaneously reduces the dimensionality of microarray data and enables ready inference of the biological meaning of observed gene expression patterns. Here we invert the GSEA process to identify class-specific gene signatures. Because our approach uses the Kolmogorov-Smirnov approach both to define class specific sig...
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We develop an analytic statistical framework for examining a variety of gene-set enrichment analysis tests. Within this framework, we describe why statistical power for both self-contained and competitive gene set tests is a function of the correlation structure of co-expressed genes, and why this characteristic is undesireable for gene-set analyses. We additionally describe why past gene-set t...
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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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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: 2020
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btaa658