We have demonstrated that it is possible to progress from transcriptomic data gathering to successful and detailed in vivo functional studies of key prioritised target genes. We have used transcriptomic (microarrays and RNAseq) and proteomic technologies to describe global changes in gene expression in brainstem, hypothalamic and circumventricular brain regions following physiological (dehydration, high salt diet, fasting) and pathological (hypertension, chronic heart failure) disturbance in rat models. These transcriptome catalogues are an important resource for researchers working on all aspects of cardiovascular physiology, and form the basis for our present functional studies. This work has relied on the development of novel viral vectors as precise tools to disentangle neuronal mechanisms and image specific cell phenotypes in the brain. Brain gene manipulation using these tools has been followed by robust physiological and behavioural analysis. Thus, we have identified novel genes involved in the biosynthesis of vasopressin in the hypothalamus (Creb3l1, Caprin-2), the physiological response of vasopressin neurones to osmotic cues (Slc12a1), and the behavioural control of salt ingestion (Rasd1 and Giot1). None of these genes would have been studied in the context of these physiological systems without the guidance of the transcriptome data.