Cryptococcus gattii is a fungal pathogen capable of causing respiratory and systemic infection with potentially fatal sequelae. Infections are treated with antifungal induction therapy using amphotericin B and flucytosine, followed by maintenance therapy with fluconazole. Fluconazole prevents the biosynthesis of ergosterol and causes toxic sterol intermediates to accumulate, resulting in stress to the cell membrane. Strains of C. gattii exhibiting intrinsic resistance to fluconazole are emerging. Chong et al (PLOS ONE, 2010) used proteomic analysis to study the growth dynamics and protein expression profiles of intrinsically resistant strains of C. gattii in response to fluconazole and compared these with strains exhibiting typical fluconazole susceptibility. Differentially expressed proteins were represented as features in a protein interaction network.  The aim of the current study is to further analyse and validate significant proteins in these networks. Using the latest gene annotation data and a new network analysis program, genes with a role in coordinating an effective cellular response to fluconazole, particularly in the resistant strain, were identified. These included a satellite network grouping ATP synthase subunits with high level of interconnectivity that had strain-dependent regulatory responses; HCR1, a highly connected hub protein that was highly down-regulated in the resistant strain. In addition, ontological sub-grouping of the network highlighted GRX5, which plays a role in oxidative stress response and was significantly up-regulated in the resistant strain. Deletion of these genes in Saccharomyces cerevisiae resulted in decreased resistance to fluconazole and various other stressors. Identifying how these cellular processes and pathways interact to coordinate an effective fluconazole response may allow new targets for novel antifungal treatments to be discovered.