I am trying to use the viper bioconductor package and having trouble figuring out which regulatory network I should use. Should I build one with aracne-ap directly on my dataset or better to use one from another dataset?
I am working on a breast cancer dataset so my idea was to use viper with the regulatory networks defined in aracne.networks as they were built on TCGA so also cancer related (and even breast cancer related). I have the impression that the example in the vignette on Human B-cell used the same dataset (dset from the bcellViper package) to built the regulatory networks (regulon from the bcellViper package) but I am not 100% sure, does someone know if it's the case?
Also when building regulatory network with Aracne-AP, I have to give it a list of transcription factors. I have seen in the paper “Functional characterization of somatic mutations in cancer using network-based inference of protein activity” that they downloaded 1,813 TF, 969 TCF and 3370 signaling pathway related genes from GO. When you build regulatory networks do you always use all of those? Or do you reduce this list to a smaller one corresponding to TFs you think are important?
Thank you for your help!