Vignette for RTN : reconstruction of transcriptional networks and analysis of master regulators
نویسندگان
چکیده
The package RTN is designed for reconstruction and analysis of transcriptional networks (TN) using mutual information [1]. It is implemented by S4 classes in R [2] and extends several methods previously validated for assessing transcriptional regulatory units, or regulons (e.g. MRA [3], GSEA [4], synergy and shadow [5]). The package computes mutual information (MI) between annotated transcription factors (TFs) and all potential targets using gene expression data. It is tuned to deal with large gene expression datasets in order to build genome-wide transcriptional networks centered on TFs and regulons. Using a robust statistical pipeline, RTN allows user to set the stringency of the analysis in a stepwise process, including a boostrep routine designed to remove unstable associations. Parallel computing is available for critical steps demanding high-performance.
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