Exploring the Monochromatic Landscape in Yeast using Genetic Interactions and Known Processes Reveals the Importance of Protein Complexes

If perturbing two genes together has a stronger effect than expected based on both single perturbation effects, these two genes are said to genetically interact. Recently experimental methods have enabled to obtain quantitative positive and negative genetic interactions [1] where negative interactions indicate buffering between genes and positive interactions suggest that the genes are part of the same process. In such genetic interaction networks, some groups of genes interact in a monochromatic manner: interactions between them are mostly positive or mostly negative. It has been proposed that these groups are functionally related and enriched in protein complexes [2]. Nevertheless boundaries and system level relationships are still difficult to define from the network. Instead of starting from the network, our new approach starts from known biological processes. We propose to evaluate the current model and study the monochromatic purity of biological processes using the most comprehensive quantitative genetic interaction data set currently available in the budding yeast that includes measurements for 5.4 million pairs of genes [1]. Method We first study the monochromatic purity of biological processes and of the connections between processes. We use Gene Ontology (GO) to define biological processes in yeast. We assess th