Finds "local subnetworks" within an interaction network which show enrichment for differentially expressed genes

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Description

Implements the method described in "Network-based analysis of omics data: The LEAN method". Given a protein interaction network and a list of p-values describing a measure of interest (as e.g. differential gene expression) this method computes an enrichment p-value for the protein neighborhood of each gene and compares it to a background distribution of randomly drawn p-values. The resulting scores are corrected for multiple testing and significant hits are returned in tabular format.

Details

Package: LEANR
Type: Package
Version: 1.4.8
Date: 2016-11-11
License: GPL-3

See help page of run.lean for a more detailed description of how to use this package. Type vignette("CCM-data") for an example showing the application of LEAN to the CCM knockout data set discussed in the paper. Type vignette("subnet-sim") for an example showing the application of LEAN to simulated subnetwork data discussed in the paper.

Author(s)

Frederik Gwinner

Maintainer: Frederik Gwinner <frederik.gwinner@gmail.com>

References

Gwinner et al., Network-based analysis of omics data: The LEAN method, Bioinformatics 2016

See Also

run.lean vignette("CCM-data") vignette("subnet-sim")