FEM (version 2.8.0)

FEM-package: Identification of interactome hotspots of differential promoter DNA methylation and differential expression

Description

The FEM package performs a systems-level integrative analysis of DNA methylationa and gene expression. It seeks modules of functionally related genes which exhibit differential promoter DNA methylation and differential expression, where an inverse association between promoter DNA methylation and gene expression is assumed. For full details, see Jiao et al Bioinformatics 2014.

Details

Package:

FEM

Type:

Package

Version:

2.1.4

Date:

2015-03-27

License:

GPL >2

References

1) Jiao Y, Widschwendter M, Teschendorff AE. A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control. Bioinformatics 2014 Aug 15;30(16):2360-2366.

2) Jones A, Teschendorff AE, Li Q, Hayward JD, Kannan A, et al. (2013) Role of dna methylation and epigenetic silencing of hand2 in endometrial cancer development. PLoS Med 10:e1001551.

3) Reichardt J, Bornholdt S (2006) Statistical mechanics of community detection. Phys Rev E 74:016110. doi:10.1103/PhysRevE.74.016110. URL http://link.aps.org/doi/10.1103/PhysRevE.74.016110.

4) West J, Beck S, Wang X, Teschendorff AE (2013) An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways. Sci Rep 3:1630.

See Also

Examples