You have already asked this question. You can use ARACNE for this, for example. You want a tool that makes an adjacency matrix.
Margolin, A. A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Favera, R. D., & Califano, A. (2006). ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC bioinformatics, 7(Suppl 1), S7.
Basso, K., Margolin, A. A., Stolovitzky, G., Klein, U., Dalla-Favera, R., & Califano, A. (2005). Reverse engineering of regulatory networks in human B cells. Nature genetics, 37(4), 382-390.