Analysing Network Models to Make Discoveries about Biological Mechanisms

Systems biology provides alternatives to the strategies to developing mechanistic explanations traditionally pursued in cell and molecular biology and much discussed in accounts of mechanistic explanation. Rather than starting by identifying a mechanism for a given phenomenon and decomposing it, systems biologists often start by developing cell-wide networks of detected connections between proteins or genes and construe clusters of highly interactive components as potential mechanisms. Using inference strategies such as ‘guilt-by-association’, researchers advance hypotheses about functions performed of these mechanisms. I examine several examples of research on budding yeast, first on what are taken to be enduring networks and subsequently on networks that change as cells perform different activities or respond to different external conditions. 1. Introduction2. Analysing Networks under Static Conditions 2.1. Networks constructed from structural relations between proteins2.2. Networks constructed using information about functional interactions3. Analysing Changes in Networks across Conditions 3.1. Active sub-networks3.2. Differential network biology4. Conclusion Introduction Analysing Networks under Static Conditions 2.1. Networks constructed from structural relations between proteins2.2. Networks constructed using information about functional interactions Networks constructed from structural relations between proteins Networks constructed using information about functional interactions Analysing Changes in Networks across Conditions 3.1. Active sub-networks3.2. Differential network biology Active sub-networks Differential network biology Conclusion