The objective of this study was to identify overlap in the response between in vitro (cultured intestinal epithelial cells of pig jejunum, IPEC-j2) and in vivo (pigs, chicken) systems upon (dietary) interventions. We used three different interventions: a high concentration of ZnO, rye, and amoxicillin. In the in vitro system we also challenged the cells by administrating Salmonella after the dietary exposure to trigger an immune reaction. Our approach was to use bioinformatic tools and data mining to investigate to what extent the in vitro system is able to predict the in vivo effects by identification of overlapping genes and biological processes affected by the intervention. Here, we focused mainly on genes, pathways, and biological processes involved in intestinal functionality and immune competence. We only found a minor overlap in genes or processes between both systems. For ZnO the main overlapping process was related to the HIF-1a pathway, whereas for rye we observed many overlapping processes related to cell cycle, and for amoxicillin the reactive oxygen species (ROS) was overlapping. ROS activates CREB activity which may lead to apoptosis. For the in vitro system we observed an up-regulation of key cytokines (IL6 and IL8) in the control samples. In the in vitro system, ZnO and amoxicillin were both able to down-regulate the Salmonella induced inflammatory genes. In the in vivo system ZnO also regulates genes involved in immune related processes (i.e. TGFß, cytokine, and chemokine signaling), whereas the amoxicillin treatment led to higher expression of genes involved in the gut barrier function. In conclusion, although we only observed a minor overlap between the in vitro and in vivo system, this bioinformatics and data mining approach showed that the in vitro system gives an impression of the in vivo system. Potentially, such an approach may yield new angles for selecting compounds for dietary interventions.