Computational Modeling of Molecular Pathways Regulating Cell Survival and Death by the &ITSigFlux&IT Algorithm

Development of new computational tools to better understand the complex behavior of molecular networks in a cell, has recently become one of the most attractive areas of research at the interface of computer science and molecular biology. In this study, the molecular pathways that regulate cell survival, apoptotic or non-apoptotic cell death is studied. More specifically, a SigFlux algorithm is used to develop a software to rank the significance of every molecule (node) for causing three different cell fates, i.e., cell survival, apoptosis (programmed cell death) and non-apoptotic cell death (NonACD). The ranking obtained from applying this algorithm identified some molecules that are biologically relevant to the induction of cell survival, apoptosis or NonACD. For example, this algorithm found that Caspase-3, one of the most important molecules in the initiation and progression of apoptosis, has the highest rank for causing apoptosis but shows a lower rank in NonACD or cell survival. This finding is consistent with empirical findings obtained from extensive experimentation on a wide variety of cells.