An interplay of physical and chemical processes governs the composition of gaseous exoplanet atmospheres. In particular, modelling efforts have demonstrated that photochemical dissociation, vertical mixing, and day-night circulation are strong sources of disequilibrium chemistry, which potentially alter the molecular abundances measured. Transmission spectroscopy can only probe a relatively small region of the planetary atmosphere -- roughly between 10 and 100 mbar -- but advective processes connect this pressure region with the atmospheric layers above and below. Given the imminent commissioning of the James Webb Space Telescope, understanding the physico-chemical connections in exoplanet atmospheres becomes crucial and timely. In this poster, we show two important mechanisms by which disequilibrium chemistry is connecting the upper and lower atmospheres of irradiated exoplanets: vertical mixing from the deeper layers, and photochemical dissociations in the upper layers. Their impact in a multi-dimensional model and for a wide range of exoplanets with different effective temperatures and stellar hosts is examined. Finally, we discuss the impact of the deep atmosphere and of photochemistry on transmission spectroscopy, and identify important uncertainties associated with the chemical abundances of irradiated exoplanets.