After thoroughly reading the GENIE3 paper (PLOS ONE, 2010), I realized that the best results on real gene expression data were achieved when using a list of transcription factors. Am I correct? If so, do you recommend always using an external TF list when inferring GRNs from real data or just defining known TFs from the expression matrix itself? If yes, at which step in the R-coding process and with which command should this be done? Thank you for your great help.
After thoroughly reading the GENIE3 paper (PLOS ONE, 2010), I realized that the best results on real gene expression data were achieved when using a list of transcription factors. Am I correct? If so, do you recommend always using an external TF list when inferring GRNs from real data or just defining known TFs from the expression matrix itself? If yes, at which step in the R-coding process and with which command should this be done? Thank you for your great help.