MARINA (Master Regulator Inference Algorithm) MAster Regulator INference algorithm (MARINa), designed to infer transcription factors (TFs) controlling the transition between the two phenotypes, A and B, and the maintenance of the latter phenotype. Expression at the mRNA level is often a poor predictor of a TF's regulatory activity and an even worst predictor of its biological relevance in regulating phenotype-specific programs. To obviate this problem, MARINa infers TF activity from the global transcriptional activation of its regulon (i.e. its activated and repressed targets) and its biological relevance by TF-regulon overlap with phenotype-specific programs.
MARINa is distributed as a set of MATLAB scripts that support shadow effect and synergy computations as well
Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A. A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol. 2010 Jun 8;6:377.