aracne.networks, a data package containing gene regulatory networks assembled from TCGA data by the ARACNe algorithm

ARACNe networks This package contains 24 Mutual Information-based networks assembled by ARACNeAP [1] with default parameters (MI p-value = 10−8, 100 bootstraps and permutation seed = 1). ARACNe is a network inference algorithm based on an Adaptive Partioning (AP) Mutual Information (MI) approach [1]. In short, ARACNe-AP estimates all pairwise Mutual Information scores between gene expression profiles, then assesses the significance of such Mutual Information by comparison to a null dataset. ARACNe then draws network edges between centroid genes (Transcription Factors and Signaling Proteins) and genes significantly associated with them (i.e. with significant MI). It then calculates Data Processing Inequality (DPI) to reduce the number of indirect connections. ARACNe-AP was run on RNA-Seq datasets normalized using Variance-Stabilizing Transformation [2]. The raw data was downloaded on April 15, 2015 from the TCGA official website [3]. We follow the TCGA naming convention (e.g. BRCA = Breast Carcinoma) to name the individual context-specific networks.