Abstract：
BACKGROUND:Network enrichment analysis is a powerful method, which allows to integrate gene enrichment analysis with the information on relationships between genes that is provided by gene networks. Existing tests for network enrichment analysis deal only with undirected networks, they can be computationally slow and are based on normality assumptions. RESULTS:We propose NEAT, a test for network enrichment analysis. The test is based on the hypergeometric distribution, which naturally arises as the null distribution in this context. NEAT can be applied not only to undirected, but to directed and partially directed networks as well. Our simulations indicate that NEAT is considerably faster than alternative resampling-based methods, and that its capacity to detect enrichments is at least as good as the one of alternative tests. We discuss applications of NEAT to network analyses in yeast by testing for enrichment of the Environmental Stress Response target gene set with GO Slim and KEGG functional gene sets, and also by inspecting associations between functional sets themselves. CONCLUSIONS:NEAT is a flexible and efficient test for network enrichment analysis that aims to overcome some limitations of existing resampling-based tests. The method is implemented in the R package neat, which can be freely downloaded from CRAN ( https://cran.r-project.org/package=neat ).
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Signorelli M,Vinciotti V,Wit ECdoi
10.1186/s12859-016-1203-6subject
Has Abstractpub_date
2016-09-05 00:00:00pages
352issue
1issn
1471-2105pii
10.1186/s12859-016-1203-6journal_volume
17pub_type
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