Gene set enrichment analysis: performance evaluation and usage guidelines

A central goal of biology is understanding and describing the molecular basis of plasticity: the sets of genes that are combinatorially selected by exogenous and endogenous environmental changes, and the relations among the genes. The most viable current approach to this problem consists of determin...

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Bibliographic Details
Published in:Briefings in bioinformatics 2012-05, Vol.13 (3), p.281-291
Main Authors: HUNG, Jui-Hung, YANG, Tun-Hsiang, ZHENJUN HU, ZHIPING WENG, DELISI, Charles
Format: Article
Language:English
Subjects:
Algorithms
Biological and medical sciences
Computational Biology - methods
Databases, Genetic
Fundamental and applied biological sciences. Psychology
Gene Expression
General aspects
Genes
Guidelines as Topic
Humans
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Molecular biology
Performance evaluation
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Summary:A central goal of biology is understanding and describing the molecular basis of plasticity: the sets of genes that are combinatorially selected by exogenous and endogenous environmental changes, and the relations among the genes. The most viable current approach to this problem consists of determining whether sets of genes are connected by some common theme, e.g. genes from the same pathway are overrepresented among those whose differential expression in response to a perturbation is most pronounced. There are many approaches to this problem, and the results they produce show a fair amount of dispersion, but they all fall within a common framework consisting of a few basic components. We critically review these components, suggest best practices for carrying out each step, and propose a voting method for meeting the challenge of assessing different methods on a large number of experimental data sets in the absence of a gold standard.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbr049