RTN - Reconstruction and Analysis of Transcriptional Networks
This package provides classes and methods for transcriptional network inference and and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies, e.g., gene set enrichment, shadow and synergy analyses.
RTN comes with two data packages from Fletcher*, Castro* et al (Nat Comm 2013):
- Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling.
- Fletcher2013b reproduces the systems biology analysis for the data in package Fletcher2013a using RTN.
To install this package and the corresponding data packages directly in R type:
source("http://bioconductor.org/biocLite.R") biocLite("RTN") biocLite("Fletcher2013a") biocLite("Fletcher2013b")
Master regulators of FGFR2 signalling and breast cancer risk
M.N.C. Fletcher*, M.A.A. Castro*, X. Wang, I. de Santiago, M. O'Reilly, S-F. Chin, O.M. Rueda, C. Caldas, B.A.J. Ponder, F Markowetz^, K.B. Meyer^
Nature Communications, in print